I've seen similar issues, and it fact it is very easy to destroy packages this way: Create a new project. Add a chart to the form. Suppose you want to look up something about TChart in the TAChart package - I ctrl-click on the identifier TChart in the editor to open the TAGraph unit. Then something happens to distract my attention, and I do not realize that the TAGraph unit is the active file in the editor. Now I want to save the new project: with TAGraph still active in the editor I select routinely select "File" > "Save As", navigate to the folder which should hold the new project, and enter a filename for the main form not realizing that I am writing TAGraph under a new name to a new location! I usually realize this issue in the next step when the IDE asks me whether the old TAGraph.pas should be deleted. But even if I say "no" - it's too late: the file already has been relocated!
So, always be at the highest level of attention when saving new files. The file to be saved must always be the active file in the editor!