Fixing one issue at different times can be very tricky. Almost every tracking system has problems with this level of detail, because you often want the single issue to remain a single issue (ie no cloning) but somehow to be fixed for different versions / branches at different times.

My suggestion to solve this effectively and simply is as follows:

• a custom field which can be applied to different projects where you want this ability
• an advanced searcher for the above field

The custom field would display checkboxes for each version in the fix versions field (ie derived data), with each checkbox indicating whether or not the issue had been fixed in that version.

The searcher would then allow you to query 3 things:

• find issues which HAVE been fixed in versions x, y, z (ie have the checkbox checked and a fix version set for those versions)
• find issues which HAVEN'T been fixed in versions x, y, z but are scheduled (ie checkbox is not checked but fix version is set)
• find issues with ALL/ANY/NO unfixed versions (ie issues with all/any/no unchecked checkboxes)

Things to think about: how the custom field gets the values from the fix version field - most likely some sort of funky Javascript.