If you are in the same situation, here is a workaround, so you can keep "file" session persistence and redeploy without loosing sessions:
1) deploy your app as usual (with persistence set to "file", e.g. <session-manager persistence-type="file">)
2) let sessions to be created
3) restart server so that the sessions are preserved in files (don't forget to specify your directory in Configuration->Web Container->Manager Properties->Session File Name)
4) go ahead and "redeploy" and let the server spit out the error I mentioned; your app will be removed, but the sessions will stay in the files (if you "deploy" instead, you sessions will be destroyed)
5) restart the server
6) "deploy" your app (you might need "--force" option)
7) enjoy your preserved sessions
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