In my experience SW cannot open (or reference) 2 files with the same name. So In reference to your (perhaps hypothetical) first paragraph - If it was me I would rename one of the "screw.sldprt" files to something else. Gotta use Solidworks File Explorer for this so it will update all the assemblies etc that are referencing that part! Otherwise this won't work.
Perhaps, however your real-life situation is that you have 100 of these "same name" files. I don't have an answer to that. Frankly I gave up using Toolbox a long time ago because I never figured out how to avoid getting error messages.
I created a new "tool box" for our company last year, and it has been a blessing. Prior to that, we used the SW tool box, and instead of using the tool box wizard thin, they would just go into one of the random SW hardware files, and pick one. They would manually add configurations they needed and it made a HUGE mess. Frequently, one engineer would get a screw out of say, the ISO folder, and use it in the assembly, but then another engineer would grab a screw out of the EN folder or something, and use that. Problem was that they all were called "screw_ai" or something.
So I have an assembly that's built the old way, and when I try to pack and go, half of the components lose a bunch of configurations, so there are way oversized nuts everywhere. I can only assume that it's because there were multiple of the same nut or whatever used from different folders.
I just tried a pack and go where I leave the folders nested, but that didn't work either. I just don't know anymore....
You cannot have two files with the same name.
Try pack and go to a folder on your PC and try it.
I have not used toolbox for a long time, too many issues.
First I have a question:
how would you create an assembly including 2 diff. parts with the same name?
I have used Pack & Go a lot over the years - however only in the last 6 months or so have I become comfortable using it. Having constant issues has been a major hurdle for me, why, see number One ?? The rest are just do's and don'ts
1. Not understanding Pack & Go
2. Pack & Go everything to a temporary Desktop Folder, (You can transfer the files later)
3. If you have interchangeable components like fasteners, drive components or other solid models (important) - make sure you uncheck the little box in front of those parts - Do Not pack & go those parts.....
4. Sometimes you would want to pack and go all the items, but then in your model you may want to hide those components and exclude them from any BOM
5. Use the Select/Replace every time, don't ever ever have the same file name stored at multiple places, one file per part - one file per assembly, period....
I made our company a new tool box of hardware with appropriate names to prevent just that.
This model was before my time here.
SWX will not allow you to have two different files of the same name in the same assembly. It will not even allow you to have two files of the same name open at the same time.
Now to the problem of having multiple fastener files with the same name. This is just a nightmare and someone is going to have to bite the bullet and a) enforce some rules, b) fix the problem.
This is exactly why we DO use Toolbox. Fasteners from different standards have different file names. With Toolbox we were able to copy the standard that applies to our parts to a new directory just for our company use. We were then able to EASILY customize this standard to include a) just the subset of fasteners that we use, b) our part number, and c) our description. These last two were done with a simple export of a spreadsheet from Toolbox, us doing a Vlookup function to associate our part number and description, and then re-importing the spreadsheet back into Toolbox. We'd be so frustrated without Toolbox for our fasteners.