As noted by Scott in reply to your post in this other thread:
http://archicad-talk.graphisoft.com/viewtopic.php?p=207198#207198
a MOD file does not contain full project information.
Think of a MOD file as a stored copy of the clipboard (e.g., from a Copy/Paste operation). It does not have libraries, views, any attributes other than those used by the stored elements, etc.
(When you open a MOD file, the 'other' information seen (beyond the MOD content) is a reflection of the last project/template file opened.)
Confusion over MOD files has existed for as many years as they have been part of ArchiCAD, so don't feel bad.
Hotlinked Modules does not refer to MOD files - but to any kind of module linked into a project. For many purposes, a PLN (full project file) is the more sensible source for your hotlinks.
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