Make sure you have the latest version installed please. With this one, deactivated cards / roster shuffling should not happen unless in some very rare cases. Essentially what happens is that when you submit the team while the server is simming, and then the new league file comes, this does not have the submitted changes yet. Now, usually OOTP tries to keep the current roster, but sometimes this fails or when you log into a different computer, then you will see the old roster potentially.
Keeping everything in sync is very challenging for the system. It seems sometimes this still fails, but we are not sure yet how & why, as the latest build (19.11.124) has many safeguards in place which should prevent that from happening.
Also, please check the Profile & Settings tab for the latest import status. If no error code is shown, everything should have worked.
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