Make clean changes package registration?

I frequently recompile the latest Julia master for experimental reasons. Occasionally the recompile fails and suggests that I do a make clean and try make again which pretty much resolves the issue. I’m wondering if the make clean has any effect on the registration of packages - I have a Julia script running on a regular crontab item and this failed shortly after my latest recompile with make clean. The reason for the failure was that Julia no longer recognized a previously registered package. Adding the package back solved the issue, so I guess the make clean somehow affected my package collection?

It might have influenced the stdlibs.