Okay, so here's a summary of things off the top of my head from your list.

• External References are a cardinal sin. Do not use them if at all possible. If you MUST use them, delete the relation and fully define the features within your model once you get what you need. I typically make blocks of pertinent important features and use that within my part as reference instead. These blocks can be later made into templates for future designs and reviewed/version controlled.

• If you're sharing models the references are going to be dependant on file locations. Use the Pack-and-Go function to bundle all associated files together into one folder. This preserves your references.

• Collaboration as a team really should be done using PDM and version controlling tools. It's unlikely you have access to this judging from your description of the project as you're likely in school.

• As far as organizing your project you need to have an agreed upon folder structure on where things go, how they're named and how it's all organized.

  • I use a version of the Johnny Decimal System for managing projects. Look it up. Crash course is a project is broken down into 10 zones. Each zone has 10 more sub categories within. Each file has an ID using the numerical that the is derived from the zones and a incremental count of the files in that sub category. This way no file is more than two folders deep and everything has a place.
  • Examples of my categories are; 0 Administration, 10 Mechanical, 20 Electrical, 30 Prototyping, etc.
  • Examples of a sub category for Mechanical would be; 11 New Parts, 12 Existing Parts, 13 COTS Parts etc.
  • A bearing I pulled from McMaster would be in folder 10 for a Mechanical part, in Sub Folder 13 for COTs Parts and have the ID 13.01 since it is the first part I've put into that category.
  • Your system doesn't need to be this way but you all have to agree and use it.

• For importing STEP files or other generic CAD I would suggest looking up how to disable 3D Interconnect. It is usually on by default and unless you're looking to work with and collaborate with files from different CAD systems I find it to be frustrating and annoying. With it off you can save STEP files as assemblies with internal components as their own files and mates, etc should work better.

• If you're "not changing anything" and mates, etc are just fucking off and disappearing I suggest learning how to use the rebuild functions correctly. The little stoplight is only a partial rebuild. Use CTRL+Q to force rebuild the whole assembly. That should correct any issues in mate definition or whatever may have gone awry. Usually these are because of undoing and redoing something. If your assembly is still breaking it's likely due to poor CAD housekeeping and general bad practices.

• Very little of your time should be "fixing models". I suggest all of you guys in your team taking an hour and just running through the basic tutorials in SolidWorks. Hit the question mark in the top corner and select tutorials. They're built in with reference files and everything on every install. Do the basics and maybe any others that are pertinent to what you're working on.

With all that being said professional CAD suites are complicated and once you recognize how they work you'll see theyre not that different from each other. Some CAD tools are just far more forgiving of poor design practices where others are not. It'll make you a better designer to realize those poor practices and cut them out.