I think that a safe bet would be 3-5 flags for a regiment in a full war's service. There were some with less and a few with more, but you would see more flags in the west if a unit changed corps in 1862-1863 and adopted the flag of that new corps.
As you correctly stated, if you lost colors you got new flags as well. I know the 16th GA had at least 4 flags; the 26th NC had at least that many too (and I am not counting company level colors here which would add even more).
Whenever I see the stuff that says, "they followed this flag all through the war," it is far more often than not hyperbole and incorrect. The 37th Alabama flag at Auburn has a similar statement for it but the pattern of the flag, Mobile Depot, did not come into use before October, 1863 so it would have been really hard for the unit to have followed that flag before that time.
Stuff like this makes our jobs a bit harder.
Greg Biggs