If you have semiautomatic weapons of war stolen and somehow they are recovered by the local constable, are they retured to the owner or destroyed by the government overseers?

You will be contacted assuming the serials trace back to you. You will be asked if you legally sold the firearms or if they were stolen from you. If you say stolen, they will be returned.

How does that square with the fact that the state treats that as a transfer, requiring a background check, and it's unlawful to transfer that kind of weapon anymore?

You see the problem.

Good question, IMO. But if you owned it before the ban went into effect, then it might be allowed to be returned to you.

It might also depend on the LE agency or agencies involved- my impression has been that some of them don’t like having firearms in the possession of the general public. You might need to lawyer up to get it returned, so it might not be worth the money.  

I’m just thinking of a few possible issues, off the top of my head. Disclaimer: I’m not a lawyer.

ETA: And there is the possibility that it could be retained as “evidence”, indefinitely.

Where in the law does it state that if a firearm is stolen and recovered by you that that is considered a transfer of any kind?

If a squatter occupies your house do you pay closing costs when they leave?

The problem is if it's recovered by the police, will they consider giving it back to be a transfer.

What law/statute is that?

It's common policy in blue counties and with WASP.

Is it legal? No.
Do they care? Also no.
Are you going to get them to change their minds with a nicely worded letter? Still no.
Can most of us afford the legal cost to beat them in court, AND survive the extrajudicial harassment and pressure we'd get put through for daring to oppose the king's men? Again, no.

You see the problem, again.