How safe is to re-use blockchain files? could they have been compromised if they were in a windows setup in the past?
What if the node you're downloading from is compromised?
The answer is the same: as long as your version of Bitcoin Core isn't compromised, it can verify all blocks again.
to avoid downloading from scratch which is hell
I used to have that experience too, but after adding much more RAM and speed improvements within Bitcoin Core, I really don't mind anymore. I'm not going to test it, but I estimate it'll be done within 2 days (on a cheap laptop that's more than 3 years old).
but a part of me is paranoid about the fact that the block files were hosted in a Windows setup for a long time...
I thought it would be a trivial thing to give a rescan-the-blockchain option at startup, but all it can do is rescan the wallet.
I've read that removing the chainstate forces a rescan, but I don't want to risk it (and I don't have the space to make a copy first). Any thoughts?
Im considering making a clean download from Linux from scratch but just thinking about it gives me an headache by how long it will take for it to sync.
If you have enough space, you can just rename your current .bitcoin and download a new one. If it takes too long, you can always move it back.