Can't save because graph is linked to external object?

One of your blueprints has corrupted reference. Create backup now, before you change anything. And in future do daily backups. When you have backup you need to find culprit blueprint (or actor).

Fastest finding method for such stuff is bisection. Ie. you delete half of actors in scene and see if unreal still crashes. Thenb you know in which half of actors corrupted one is. And you continue until you find that one crashing everything. Yes restoring from backups is slow, so consider getting SSD for unreal (backups are cheaper).

If you rule out corrupted actors, you may have corrupted blueprint class. So almost same procedure, but this time delete blueprints one by one. You do not need working code, all you need to see where is that corrupted reference. When you found exact actor or blueprint that crashes your project, restore everything from backup and delete just that one crashing.

Then you need to recreate it manually, do not copy paste it may recreate crash. I have powerfull enough PC that i can open 2 unreal projects (in 2 editor instances) and just copy over stuff.

And remember to make backups either manual or use version control.