As far as I know, moderators can cancel tag synonyms and such things happen occasionally. (I've seen some threads about removal of tag synonyms here on meta.SE.)
How will the questions be tagged after the removal of the synonym? We have many questions tagged (master-tag). Some of them might have been tagged by (slave-tag) at the time when the synonym was created. Some of them might be tagged (master-tag), but they got this tag after a user explicitly typed (slave-tag) when entering the tags.1 After removing the synonym, do all question keep the (master-tag)? Or do some of the questions get the (slave-tag)? (For example, the two types of questions mentioned before seem like a reasonable candidates.)
An additional question: Does it make a difference whether the two tags have been merged2 or only synonymized?
Originally I have asked this at a local meta but this is probably a more appropriate place (and with a better chance to get an answer).
1Number of such posts is shown in the list of tag-synonyms.
2From what I have read here it seems that merging is independent from creating a synonym. But it is sometimes done when a tag-synonym is created. Based on the answer to the following post, it seems that there might be a difference: Need a rollback/undo for tag synonym merging.