Merging a SH Plan with a Non-SH Plan (What to look out for?)

Alright, so my question concerns the merging of a safe harbor plan with a non-safe harbor plan and the potential pitfalls which may arise. 

We have a client who is currently involved in a corporate acquisition, not yet known whether a stock or asset sale, and their company is acquiring another company who currently sponsors a SH plan. Note, our client's company currently sponsors a non-safe harbor plan. I would like to provide them with a few bullet points of what to look out for and potential issues which may arise as a result of the merger. Based on my research, the IRS hasn't really provided guidance in this area and it appears the safest thing to do would be to move the participants of the seller's plan to the buyer's plan at the end of the year. However, playing devils advocate, what if they were to merge mid year? Also, how would deferrals be treated with respect to the safe harbor plan? I would greatly appreciate any input.