Yes there were two crises that happened

The first one happened in 2010-2011. More details in a future article.

Here is a timeline of the 2nd crisis that occurred 2015-2017

Sidenote: This is a response via a truly uncensored explanation of the sugar-coated/completely baloney claim/statement in a recent “sermon” by Senior member Roberto Flores:
“As time went on in 2014-2016, many of my fellowship members left the ministry. I was very bothered by this because each person in my fellowship was very dear and precious in my eyes, and we all worked together closely like a family.”
Source: http://www.shepherdschurch.org/Current-Message/eastersundayapril162017 [The original link is broken, however, I was able to archive the message before it was taken down]
**Disclaimer: All the names in this article are actual names. The intended purpose of this article is to give a general overview of the “crisis” that happened recently. No personal information has been disclosed.**
2015-2017 El Camino UBF Crisis Timeline
Background: In 2004, John Baik  start his own chapter and its membership begins to grow rapidly. By 2010, issues begin to come to light in the church, and long-time disciple, G leads an exodus of most of the members from the church, about 15 overall. The few disciples who chose to remain in the ministry went on to become the new Senior leaders. This was the First Crisis (or ‘exodus’) experienced by the chapter.
By 2014, an entire new generation of shepherds had been established, and the recruitment numbers had recovered since the First Crisis. At this time, Shepherd’s Church was going through a period of strong growth.
January 2015: C , who had been a member of Shepherd’s Church for four-five years quietly leaves the ministry and is soon pretty forgotten by the rest of the congregation. G.G also leaves the chapter.
April 2, 2015: Eric Navas starts a blog about the truth behind the chapter. This i the first time in the history of the chapter that their atrocities and darkness has been recorded and brought to light. His bible teacher Rothrock finds out about it and demands for it to be delete. Eric instead privatizes the blog and its put on hiatus.
September 2015: ___________ suddenly and unexpectedly leaves the ministry for unknown reasons. His departure is a shock to his fellowship members and to the rest of the church. He is a mainstream student (Caucasian White), so his departure is considered to be a huge loss for the ministry. His Bible teacher, Mary Zavala supposedly goes into a period of deep depression over this and remains emotionally and psychologically wounded by the experience.(It is possible she could have faked it)
Following this event, her fellowship goes into a period of decline over the next year, losing about eight members total. In the meanwhile, however, the membership at El Camino UBF continues to grow and new disciples are established.
January 2016:  J.A, a mainstream student who had been living in the sisters common life, quietly leaves in the middle of the night, never to to be seen or heard from by the ministry again. 
June 2016: ____________, known for his large Bible study numbers and having raised four disciples suddenly stops showing up at church services. Despite this, however, his three remaining sheep stay in the ministry.
July 2016: A.B quietly leaves the ministry for unknown reasons.
During the month of July, a Pilgrim’s Progress symposium is held with all of the new and growing disciples within the ministry. It is considered to be a huge success and God is praised for doing a great work within the ministry. This is the point where the chapter has reached its peak of success. The month of August passes by quietly as the church prepares to begin a new recruitment effort as the fall semester starts.
However, during this time,  Eric Navas contacts wikigoat and resumes his blog privately on the activities going on at Shepherd’s Church. Around this time, several former and current members individually contact Brian Karcher to express concerns that they are having with the ministry. Shortly after this, a group of former members begins to meet together to discuss their experiences within the church and to help one another to recover from the spiritual abuse they had received.
Early-Mid September 2016:__________ contacts his three remaining disciples within the ministry and informs them of all the issues going on and their need to leave as soon as possible. The three disciples decide to leave quietly without informing the church leadership.
Later that week on Friday night (Testimony sharing night) the former members and the three disciples who had left the ministry all meet at a restaurant for fellowship and mutual support. The church still does not know that the three disciples had decided to leave.
As evening approaches, the three disciples begin receiving numerous calls and text messages from the church leadership harassing them as to where they are. The three disciples ignore the messages and continue enjoying an evening of fellowship with the group.
The next day, a Fellowship Leader, Anthony Zavala, from the church goes to the workplace of _________ and demands to know what happened to the three disciples. __________‘denies’ knowing anything.
 September  11,2016:  several of the former members want to expose the church to the rest of the members, and debate on the action to take.
September 12, 2016: However, Mark Johnson spends two hours writing an email listing all of the unbiblical things happening at the chapter. At 8PM that night, the email is sent out to over fifty members of the church. By 10PM, John Baik orders everyone to the chapter to discuss the email. At the secret meeting, it is decided that everything should be covered up and all contact broken with former members.
Suddenly, C.G, A.B  and another former member go into the church and confront John Baik and the church over all the issues going on at the church. The event is audio recorded. They are soon ordered to leave the church.
September 13, 2016:  C.G. and ________ meet with John Baik to discuss the issues in the church. The meeting goes nowhere as John Baik refuses to acknowledge the issues and opposes any changes.
September 16, 2016: John Boos, John Baik’s right hand man sends an letter officially banning all ex-members.
Late September 2016: Surveillance cameras are installed at the chapter. An unofficial/unspoken policy is set in place: Any ex-member or outsider that sets foot at the chapter that doesn’t have John Baik’s approval is to be arrested and treated with extreme hostility.
October 31, 2016: Eric Navas leaves the chapter for good at the beginning of that month. Later that same month he sends the Taylor Bell recordings to Sarah Baik in hopes of support, understanding or at the very least a chance to share his side of the story.
December 26,  2016: Rothrock sends Elva Aldrete to harass Eric’s family and coerce his sister into going to the 2017 New Years Conference.
Late January 2017: Eric confronts Rothrock at CSUDH  about the recent events. Rothrock denies any involved and like John Baik refuses to acknowledge any issues/concerns. [Sidenote: The church held a New’s Year’s Conference in January 2017, however only three visiting sheep attended–an enormous loss for a church known for its high recruitment numbers. This was widely seen as a rebuke from God against the church for practicing “heavy shepherding”.]
February 2017: Eric Navas publishes his first article on the chapter here on UBfriends and continues to do so to this day.
March 1, 2017: Eric Navas coincidentally comes across across Rothrock while going to class only for him to threatened to call the police on Eric.
Over the following months, several more members leave the church. Overall, during this crisis, 20+ members left the church. 
May 23, 2017: Eric Navas publishes part 1 of his narrative.
Early July 2017: Baik relocates the church in response to the events mentioned above.
July 5, 2017: An unsatisfactory report is made to UBF regarding the 2nd crisis
July 13, 2017: Eric Navas publishes part 2 of his narrative.
Late 2017:  Lois D. Baik, Taylor Bell, and Elva Aldrete leave the church. The exact reason is unknown
Conclusion: El Camino UBF shrank in its membership size significantly after the Second Crisis. They haven’t and won’t be able to recover ever again. Currently, the church is going through a period of stagnation due to being unable to get any newcomers since Another crisis is expected to occur by 2020 not just in that chapter but in UBF as a whole. Most of the members who left during the Second Crisis have since moved on with their lives. Many have rejoined the evangelical Christian community and continue to serve God. Others are still recovering and not ready to go back to church yet, while some are done with Christianity and religion entirely.
Additional Note: Roberto Flores was present during the secret meeting where Baik threatened to have the ex-members arrested including Ashley, the woman mentioned in Boos’ letter. She was in fact part of Flores’ fellowship.