I have been struggling with this very problem the last two days reading through pages and pages of discussions on this issue and not one solution worked. By chance I remembered in Auto Cad that changing file paths in the options could really mess with something like plotting if the pen file was not where you were pointing cad to go look.
for those of us that are coming from cad this is kind of similar just in a different spot. When you open a file there is the option to click on projects make sure you have the correct project folder location selected, once your in the project folder selection window click on a project. There are options below the list of projects to select, expand the libraries path.
Make sure the path is pointing to the library folder created for the project. Then make sure that you do not save any files to that location. Inventor will atomatically save parts you place in an assembly from the content center there, and as someone somewhere wrote you cannot edit inventor lib files.
Hope this helps
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