That question can probably only be answered by debugging it.
Make a backup of your project. Especially the LPI and LPS file.
(The LPS may be in the "primary config path" directory / depends on your settings)
If you then remove nodes from the XML of either file (mainly setting related, not file/unit), and find the part of the xml that makes it go away / come back.
Otherwise, how private are the project files?
That is, the lpi and lps? (Hoping that it can be reproduced with just those 2 files)
Then you can upload them, and maybe someonen with more knowledge can have a look at them.
(the contain: unit names, compile settings, build modes, watches, ...)