What software do you use ? We use bwa/samtools/varscan/bcftools and we've reprocessed old data right from the fastq files a few times. So far we haven't gotten different results.
I encounter an error that I can't currently find exactly but it happens when running mismatch_profile from the RSeQC package. It reports a mismatch in the length of the cigar notation and the actual read inside a BAM file. Lately I have become 99% sure that this sometimes happens in files that did not show this error before (we reprocess a lot of data from time to time). I suspect it is bit flips because I think bit flips can easily go unnoticed, but not in this case, because the cigar notation is a shorter description of the actual read and they should thus match. The mismatch signals a change in the file that occurred without us touching it.
Hmm, yeah that is odd! Maybe its a bug in the alignment tool?
It's not reproducible and I say I'm 99% sure it comes from bit flips is because I know with 99% certainty the process did finish successfully on a file at some point but then failed several weeks later, on the same file.