I live in country A, but use a server in country B.
I worry that when I visit websites where my identity is know (for example my University Microsoft), whith the VPN IP, I become deanonymised.
Is this a valid concern?
If you’re logged in, then yes, the website knows it’s you.
They might not know the original IP address that your VPN is hiding, but they still know that it’s “you.”
Yeah, if you log into any account, the account service provider will know its you no matter the IP you are connecting from. This isn’t de-anonymization because you would be voluntarily logging in an account.
Whether it is a valid concern or not is upto you depending on what concerns you.