That sounds like a right mess.
Going by what you're saying, if the data on those systems was altered at all once it left the suspect's / owner's hands, then it is very likely that continuity of evidence has been irreversibly compromised and its provatory value will be particularly scarce if any.
Mind, faced with a competent judge or an expensive lawyer IT evidence tends to have very little weight anyway and would normally be used just for corroboration. It is very difficult to build a strong case from it.
But one thing that allegedly happens in places where the police are poorly trained and/or poorly supervised (UK and France, notably) is that the plod try to play judge & executioner: "he must be guilty though we can't prove it (or we just don't like him) so let's teach him a little lesson by fucking up his stuff". Yes it is a sad state of affairs.