I would first add the polyquat--FC will drop, all the way to zero probably. Then raise the FC again.

Normally, we don't worry about chlorine damaging vinyl liners unless FC is above 15ppm (but that depends on the CYA level, too). I don't know how that affects vinyl covers--there's different kinds of vinyl.

Still I would, after the polyquat drop, raise FC to a minimum of 10 just to be safe. Still, below 60 you shouldn't see algae growth.

But it's your pool--the final decision is yours.