I just lost an almost 600 day streak because I decided to use mobile logins for a couple of days cause I was travelling. Used to work fine, did everything right, both accounts are synced to the same gaijin.net account.
It should still work as normal. It essentially “pauses” the login streak while your using the mobile version and doesn’t progress it until you log back in to the regular version of War Thunder, at which point it resumes from the same streak number as before starting the pause when using the mobile version.
If you’re certain that something went wrong i recommend contacting support. You can find support and instructions on how to contact them here: https://support.gaijin.net/hc/en-us/articles/360000262858-How-to-submit-a-support-request
I don’t know if they will be able to do anything but it’s worth a try.
Has always worked for me, not sure about now?