There is an interesting article on managed metadata column limitation from sharepointanalysthq wihch describes many interesting limitations. That list is really useful. There are some useful suggessions that I want to add to the list:
1. Never export list/document library with managed metadata as template with data in order to copy it locally or othre places. Main reason behind the same is, managed metadata columns has term store, term set etc defined and they will not match in the destination managed metadata application and can cause problems
2. Never stop/remove taxonomy updater services, specially because they are responsible to make sure your manage metadata columns are having consistent and up-to-date data all the time.
3. One of the option for moving list/libraries with managed metadata column along with preserving all it's IDs is to use http://spdeploymentwizard.codeplex.com/ utility.
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