I had the same problem after re-upgrading my expired Dynalist Pro. It had worked before, but immediately after upgrading I got the following e-mail:
We weren’t able to save your backup to Dropbox.
Here’s why: Access to your storage account has been revoked.
I unlinked and linked Dropbox from my Dynalist Desktop app, but the problem remained.
Next reinstalled Dropbox and noticed after your problem description that the Apps folder was on my local Dropbox folder, but not on the Dropbox server.
I logged in on Dynalist server (not the desktop app) and unlinked/linked the Dropbox folder again. Now it’s present on both Dropbox server and local folder.
Hope it will work at the next backup run.