Which importer tool were you using?  Lr’s Aperture Importer? Are your photos managed or referenced?  How large is your Library or do you have several Libraries? If you move all of your photos into a single referenced folder, you should in the least be able to import them directly into Lr by selecting the folder and using Lr’s IMPORT process (not the Aperture Importer), then choosing ADD.  At least that way Lr will recognize them.  Of course, all of your adjustments, metadata, star ratings, won’t be recognized.  If you have a large library, some people had success with splitting them up into smaller libraries and importing them piecemeal.  I guess we need more info to see if we can specifically give you some help.

I didn’t use the Lr Importer but bought Aperture Exporter (~$12) instead and used it to move my photos.  90% of my photos were referenced with only my 2014 photos being managed.  With AE they were copied and I moved them all into a single new folder and then that folder was “imported” into Lr.  Now all of my 2015 photos go into that one new folder.  That did create a duplicate of my photos but they are now all on a large mirrored external HD and I could easily delete my original referenced folder if I ever need the space.  However, that does not help you with Adobe Lr’s importer.  Hopefully someone who has used Lr importer could chime in.  If not try calling Adobe support??  Good luck.

Florian