The unretire is not so problematic. The main issue is that all of the visitors will be "Hostile". Easiest way to deal with them is to kill them. Most of the rest of the effects are not bugs -- they are intentional: all your booze is dumped. Animal/dwarfs in random locations. Work orders are all deleted. Most things in bins and barrels are dumped. Random items will be decorated and gems will often be used up. Sometimes random dwarfs will leave or join your fortress. I've even had goblins join my fortress. There are a few more documented things in the wiki which I forget, but it's all pretty minor. Absolutely make sure you have some plants around when you retire so that you can begin brewing immediately after untretiring. After that it takes a couple of months to clean up.
The other kind of minor bugs that I've encountered are: If a caravan was scheduled to arrive, then usually the crew will join your fortress as residents (not citizens). They will petition for citizenship as normal though. It's just a pain because they hang around in the tavern all the time for the first 2 years. If a dwarf was hauling something when you retired, sometimes the thing they will be hauling will be essentially untouchable. The way to fix the problem is to build something where it is. This will cause the dwarfs to move it. Once it is moved, it will be normal again.
I think that's about it. I once retired and unretired a fortress every year for 6 years running. Really, no major problems. Just annoyances.