Anyone else experienced this?
I dual boot Linux/Win11 and use profiles in Chrome for work and personal. It clears cookies in all profiles.
I've tried to delete/recreate the Chrome profiles and again login to all websites but the issue persists. Just now it cleared everything again.
The only extension I use is uBlock Origin (with a bunch of whitelisted websites and this list doesn't get erased when the cookies are erased).
It seems wonky that Chrome would be going out of its way to delete stored cookies separate from their expiry timer, but much more plausible that Google is invalidating session tokens on the server side and making you re-authenticate.
Otherwise maybe contact yubico support or open a ticket on the Google chrome forums, they provide pretty useful advice.