I'm working on SW 2016, and I'm having a problem with an assembly, in the "featuremanager creation tree" my component references are in light gray. And when I hover over it, I get the following message: "The internal file ID of this component does not match".
This is because you had to rename a part by the same name as the original part. I think you need to rename it and then you right-click and select "replace components"
You have several times the same component with the same name in different places on your disk.
By default SW will look for the component that is already open, hence the internal ID message.
You had to open an assembly, close it (or not) and open your new assembly that didn't point to the same files.
You also had to check "don't ask me again" in the dialog box that offered you to delete or accept the component whose l4ID didn't match. (to reactivate the dialog box you have to check it in tool/options/messages)
When you restarted, you emptied SW's memory and your assembly naturally went to get the right components.
You could have just closed SW and reopened it without restarting the PC, it would have worked just as well.