To reproduce:

• assign 2 different Termcollections to a task
• do termtagging
• remove one of them
• redo the analysis/termTagging

Result:

Term-Markup of the removed termCollection stays in the segments. This should not be the case, in a retagging all existing termMarkup should be removed.

What would make sense in a retagging though, if no TermCollection is removed, to keep the existing mark-up and only let the termtagger retag those terms, that are new in the Termcollection since the last tagging. And remove those, that are deleted from the TermCollection (or changed in status, so that they should not be used for termTagging any more). Yet this is just an information to keep in mind for development, nothing to implement now.