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I have 2 users that are frequently "losing" files. I'm 99.9% sure it's due to them deleting workspaces before checking in files or deleting the workspace contents. Are there any log files that I can reference to confirm what they are doing to lose this data?
I assume your users are using Creo, I think you can use trail logs to check also you can enable applogs and bsc logs to view whats happening between Creo and Windchill.
Looking the URLs from the users by filtering login name in Apache access log will be good start.
There's also the option of checking the Methodserver logs within Windchill. Go Site/Server Status/Monitoring Tools/Log File Viewer, select wt.logs.dir and search for their account name in Content Search String, also try to carefully pick the Log Age so you don't get too many results. That should show a great deal of what they've been doing.