Merging terms causes tags to be erased

This is more of a notice than a specific bug report. We just tried taxonomy manager on a fairly complex site with a long taxonomy (where most terms have a few levels of parent terms). We have active tags enabled for input and a host of other modules.

Active tags allows people to free-tag in addition to select tags from an autocomplete. This created a few duplicate terms for us, so I tried using Taxonomy Manager to merge similar tags together. I would select the extraneous tag, click merge, select the tag from the autocomplete that I want it to be merged into. The problem is that only some nodes ended up with the new tag. The old tag was erased and I ended up with some nodes with no tag at all (I noticed this when the extraneous tag had 7 nodes, the original tag has 22 and when I merged them, there were only 27 nodes tagged with the original tag). I then tried it with a single node (which had a single tag) and that ended up with no tag at all.

So a word of warning that this feature may cause the loss of tagging information for nodes.