I tried to use git annex assistant: I can get files to be backed-up on a server, but when doing sync between 2 different machines it has never worked (I've been doing the xmpp-setup dance multiple times, and it's especially painful due to having 2factor auth enabled on google)

I'll have to try using plain git annex from the commandline to try to understand what is going wrong (I already used it to clean some repositories that the assistant was refusing to delete)

PS: I tried it with 2 machines in the same LAN (both linux... though one of the 2 distros had a slightly older version of the git-annex package)

no doubt it would be my first choice if it had proper windows support, but last time I checked that was still lacking

SHA1?

It's configurable.

The default MAC algorithm to be applied on the filenames is HMACSHA1. A stronger one, for instance HMACSHA512, one can be chosen upon creation of the special remote with the option mac=HMACSHA512. The available MAC algorithms are HMACSHA1, HMACSHA224, HMACSHA256, HMACSHA384, and HMACSHA512.

Don't worry, git-annex uses SHA1 just as a checksum, not for cryptographic purposes.