If the user chooses to have auto-reimport check on engine startup they are greeted with a dialog that states
“We noticed that your auto-reimport settings are set up to detect source content changes on restart. This might cause unexpected behavior when starting up after getting latest from source control”
If the user chooses the “Don’t show again” checkbox and chooses ignore, it will still appear every time they start the engine
Thank you for your report. I was able to reproduce this issue internally and have entered a bug report as UE-18623. As we investigate a solution to this issue I will keep you posted here.