I can't answer that directly but can only imagine what you may have done.
A package is a like a box or paper bag you can just throw things into, in this case unit files that all belong together and many times they are stored on your system in a folder for each package you have installed as unpacked files.
It's possible you pointed a path to that package folder using the additional path settings in your project, which normally are used to point to some additional files elsewhere for your project.
Basically, using the Project inspector your project can create a catalog of packages which point to folders that contain the needed associated files.
One step that should be taken and that is, if you archive projects, you should also create a folder in your project folder where you can store the package file of each one you are using for that project that isn't normally installed by default for the IDE.
This is a way to be able to open your project later on and re-install the package or at least have reference to it.
Also, if your project is important to you, you could also store the current version of the IDE compressed when you archive it.
Jamie