That's the problem, you can't be sure it will always be 100%. If your equipment is very good then chances are more. I've read cases where faulty cabling could flip bytes here & there, bad memory could also do that. Bad HD sectors tho much rarer nowadays can also do the same.
I was suggesting a method to use the checksums stored internally in both formats as a quicker way of achieving the same. Say you start from APE or FLAC, both these formats contain a checksum, by default for integrity testing, then you convert either to Wav and finally compress to either. The resulting lossless file will also contain a checksum. If it can be shown that these checksums are equivalent, you get to see an OK, which truly means your conversion was 100%.
Think of it as a *secure* lossless conversion.
The reason for this is you are storing in lossless and the idea is provided it was ripped securely, then you have an identical or lossless rip in which ever lossless format you choose. There is a certain expectation that a conversion would also be 100%.
It remains to be seen whether the checksums used by APE or FLAC are even similar enough to be compared in this manner, it just saves an extra decode to wav from the target format. If you have a large amount of files to convert, then it could shave off 20% of the time.