Well, in my opinion is very important and all is related with the links....because you can have problems when you will try to load an assy.
It also depends if you are working in a PDM system or with files on hard disk.
On a hard disk you can avoid conflicts by declaring the Search Order in a way so CATIA will load what you want first but in a PDM system you will never do a Check In if there is already a part with the same UUID in PDM.