I think Osoyoung will agree, timing makes all the difference as to how much root work you can do. At the end of winter as buds swell for spring you can be pretty agressive.
End of summer, when night time temperatures begin to drop below 65 F, there is a flush of root growth. For my zone 5b region this time period is Aug 15 to Sept 15. Repotting at this time can be agressive, IF you provide winter protection from extreme cold. Keep them above + 23 F ( - 6 C) for winter, if repotted in August or early September. Normally a flowering quince of the larger growing 'Toyo Nishiki or C. speciosa types can handle cold, mine survive -17 F (- 25 C) simply under the bench with tarps on 3 sides to block sun & wind.
But a recently repotted quince won't have time to fully mature and harden off a root system. So winter protection would be appropriate.
Flowering quince will root from cuttings, even large diameter cuttings will root. This means with good after care (humidity tents, etc) you can just about totally remove the existing root system, and it will grow a new one. But it is risky, the more you remove the more you stress the tree, and the longer the recovery time. With mine I'm usually pretty gentle with my quince root systems.