In our Inventor 2012 projects we have multiple .ipt files with the same name that are located in multiple directories. For example:
\projectX\part1.ipt (a 6 inch bar)
\projectX\subpart\part1.ipt (a 9 inch bar)
\projectY\part1.ipt (a plate)
When I import an Inventor (.iam) file to Navisworks 2014 the wrong .ipt files are used. I suspect that Navisworks don't know where to find the file like Inventor does and does some kind of a path/file search starting in the current path. It seems like the first hit (based on file name) is accepted by Navisworks and used in the result. So instead of the part1.ipt with the 9 inch bar the 6 inch bar is used.... or the plate....
A workaround is to change all project so that every .ipt has a unique name but based on historical data (old projects) and combination of multiple designer projects this is very unpractical in our situation.
Is there a solution to this problem so Navisworks "knows" the completed path of a .ipt file when it runs the import? I would expect something the same as "pack and go" with Inventor with the option "Keep Folder Hierarchy"
You may try the "Using unique File names" option in Inventor in order to resolve the duplicates issue.
See here:
http://usa.autodesk.com/getdoc/id=TS14130027
Another option would be to use the Pack & Go feature - as you have already mentioned - and check the option for "Create Single Folder". This will prompt you to rename the duplicate files when copied into a single folder.
I hope this helps.