Yes, it can be quite complicated when you are dealing with 1000's of groups to replicate the users, so much so, I ended up writing an application specific to manage migrations, that was used to orchestra migration batches and supported discovery, scheduling, and replication of details between domains, this included the replication of group membership in both directions.
Why I wouldn't change the groups type: when changing a group from domain local to universal, you are changing the scope of the group, and what members you can be added to the group, i.e. you will no longer be able to added users from externally trusted domains, which could impact how users access resources pre and post migration, which might require you to change the access model for all the resources that use these groups. The another issue, in this scenario, if you have a multiple domain forest, this change will increase the replication traffic, as now all group membership changes need to be replicated to the global catalog on all domain controllers in the forest. This is not a problem if you have a single site, but if you have multiple sites in different countries, this could impact bandwidth requirements. The other issue which is hard to define, and is normally unknown until after the change, is hardcoded dependencies normally associated to applications.
I hope this helps.