I don't know if anyone else has struggled with this issue but I found a relatively simple solution to a problem that has plagued my workflow for days.
The Setup:
A portable 4TB HDD contained an assembly cut of a feature film I needed to polish and finish, however the folder structure was atrocious and the speed of the drive was poor - awful working conditions.
The Solution:
Transfer the entire folder structure to my RAID for cleanup and faster editing, sounds easy enough.
The Problem:
Loading the project file from the RAID would require new links to source footage (it was searching for the external HDD, but this is not what I wanted) so re-linking media (1800 or so files from the RAID) would get to what appeared to be 100% complete and then stall for infinity until I force quit PremierePro.
I had considered using the Project Manager inside PremierePro but being stubborn and already having transferred the 3 odd TB of data I decided to knuckle down and figure it out.
My Solution:
Open project file from RAID (no external HDD connected), when link media window pops up, uncheck the "link other files automatically" box, locate and link the first file in the list and then press CANCEL.
VOILA! The timeline opened perfectly with every piece of video and audio USED in the timeline working and linked (how I do not know). The only caveat to this workaround is that using unused footage would require a manual re-link but this can be performed en masse for whatever bin you're using. The upside is that once you re-link files when the project has loaded correctly, these files will be permanently linked to your new source location (for me on my RAID).
My Apologies:
If there is an extremely simple way to just point and shoot around this issue I don't know about then forgive me, but if anyone has been battling with this malakias I hope this helps.