Comment 41 for bug 1712579

The solution as quite simple.
Dirty bit for each zone.

The essence of the "zone thing" is to tell the router if a track segment is inside a zone or not.
I presume it is a highly optimized routine called to decide the fate of an action (denied or not).

So, as soon as you asserted an action inside a zone, flag it Dirty Zone.
The dirty flag is set by zone edit.
The dirty flag is saved with Zone data.
The dirty flag is cleared by refill only.
For simplicity Ctrl-Y never touches it.

Once a dirty flag is set, you even need to bother check.

Needless to say gerber function is allowed with a big warning.
The flag can also be used to trigger a forced rebuild with "CleanUpTrack&Vias"