Most emails have disappeared from the folders I have set up

The Emails are still there in the Gmail web GUI though. Is there a way to refresh? Do I need to remove the account from EM Client and re-add?

If you right-click on the GMail  All Mail folder in eM Client, and select Properties > Repair, that should force a resync with the server.

We have the same problem. We note that this repair button carries a warning. Is there any risk of deleting or moving emails on the google server?

The warning refers to local messages, not those on the server. What the repair does is to delete the local message cache, and then download everything again from the server.