OK my problem seems to have solved itself. I'll describe what happened here for other users.
Like the user above I uninstalled Boxcrypter without decrypting the files (I thought this would happen as part of the uninstall but it does not). There should be instructions in the Help about this as I noticed several users have had this question in the forum.
When I found my files were still decrypted, I reinstalled BoxCryptor but it was now showing Google Drive instead of a Dropbox folder (which is what I had before). I delinked Google Drive but couldn't figure out what to do next. I now had an empty Boxcryptor drive.
I was panicking and trying to find help here, with no success as there seemed to be no way to decrypt the folder if you can't access it in Boxcryptor.
I'm not sure what I did or if it just needed time for something to refresh(?), but a little while later I look at my drive and the dropbox folder is now there! Now I could do what I should have in the first place - right click, pick Decrypt.
Now I uninstalled Boxcryptor and my folder is OK.
By the way, the reason I decided to uninstall was last time I tried to login on my computer with a PIN, somehow it had changed to requiring a password Until I figured this out, I thought I'd lost access to my files. That made me afraid that if somehow I lose access to my Boxcryptor account, i will lose my files. This seems like a higher risk than leaving them unencrypted.