1. Transition Period
Actually, the plans never need to merge. The "transition" rule simply provides relief from having to count *all* employees of the controlled group for coverage testing of each of the plans - until the end of the transition period (subject to being able to pass coverage individually on the day before the merger took place). If the plans can pass coverage after the end of the transition period, or can pass coverage on an aggregated basis after the end of the transition period, they can remain "un-merged." Nothing in the Code ever requires plans to merge - it just has various testing implications depending on who is covered by each of the plans, and what the (testable) benefits are in each plan.
2. VCP
First, see above. The plans may be able to remain separate (or be tested on an aggregate basis) and still be viable. Second, your concern of tainting the clean plan is valid. Consider instead of merging the plans (if necessary), simply freezing the dirty plan while seeking the IRS's blessing of the VCP filing, and letting all the employees participate in the other ("clean") plan - amended however the employer sees fit. When (and if) the IRS rules on the VCP application, the "dirty" plan can be cleaned up and merged into the other plan.