Using SSO with GIT causes the Designer to sync before it's logged into the Clover Server and subsequent conflicts

My team recently switched over to using SAML-based authentication so we could use our company's single-signon system (Okta) to log into our development CloverDX server (version 5.5.0.21, same as our CloverDX Designer version). Each morning after we VPN to our company's intranet and start work on CloverDX Designer, we get a stack of Server De-sync errors when it attempts to refresh our developer sandbox; CloverDX Designer then brings up a browser window to refresh its connection to the server via SSO, after which that browser window goes away. We then need to hold down the Esc key to clear away all the Server De-sync error dialogs, then refresh the sandbox again and clean up any lingering changes there that might have been applied by the desynchronization; we use git for source control so this usually involves undoing all the changes to bring it back to a clean slate.

Is there a way to avoid having these De-sync errors pop up? It appears that this is related to our SSO sessions expiring on a daily basis, and that Designer is able to re-establish a connection and a new session, but for whatever reason that only happens after it gets confused about the files that it was not able to synchronize. Occasionally issue happens in the middle of the day as well, but I have not been able to identify the circumstances under which that might occur.