Hello Chris and thanks for compliments,
Indeed, changing folio resets the incremental conductor's counter of the folio formula because you lose focus on it when you change folio.
It seems that the problem is very old, I can reproduce the same behaviour on old versions of QET..
Curiously, I don't remember anyone reporting this bug before. Maybe working differently. 
With my formula don't use %id/%total folio label name, see: https://qelectrotech.org/forum/viewtopic.php?id=2365
scorpio810 wrote:Hi,
btw use "%id" instead "%id/%total" in your titleblock's pages, otherwise you will see Xref like this "(folio_label/total_ off_folios)-(line number)- (column_number) etc.
So, is easy with ctrl +f in and then folio section to change "%id/%total" by "%id" in all project's.