This step should only need to occur once. Although you need a different provisioning file for each project, your Account Certificate should remain the same between any projects published with Thunkable.
Once you issue a new certificate, that will be good for a period of 1 year from the date of creation. You should be able to publish as many apps as you want with that 1 distribution certificate for you (the publisher) and 1 provisioning file per app (per published Thunkable project)
A certificate is specific to the email account that was used to create the certificate. I.E. If you are helping another Thunker publish their app, you would need to log in and publish from that users account using their certificate.