I really don’t understand your focus on errors, it really has nothing to do with FLAC or lossy compression schemes. The decoders will very clearly fail if there is corruption or errors.
MQA is destructive right from the original downsampling through the folding and finally via the upsampling to restore the original sample rate. It isn’t done in error but by design.
I agree the master is by far most important and 16/44.1 will deliver a good master wonderfully.