Can I still claim the principal residence exemption if the flipping rule applies to my home sale?

No. If the flipping rule applies to a sale, the principal residence exemption simply isn't available for that sale, even if the home genuinely was used as your principal residence for the whole time you owned it. The flipping rule works as a deeming rule - it overrides the normal principal residence exemption analysis entirely for that specific transaction, rather than competing with it as an alternative option you could choose between.

This is one of the most important things to understand about the rule, because it means the usual facts that would normally support a principal residence exemption claim - that you lived there, that it was your only home, that you meet the ordinary tests - simply don't matter once the flipping rule applies. The only way out is if one of the specific life-event exceptions applies to take the sale outside the flipping rule altogether; if that happens, the sale reverts to being analyzed under the normal rules, and the principal residence exemption can potentially apply as it normally would. Given how much this can affect the tax owing on a home sale, it's worth checking the holding period and exception list carefully before assuming a short-held home sale will be exemption-eligible.