First rule out any glitches in the model/software (unlikely this is the problem, but worth ruling out)
Save and close the software (not just the model but the entire program). Reopen and see if the issue persists.
Restart your computer and see if the issue persists.
If you can, see if the issue persists on someone else’s computer (you could attached the model and I could test it out)
Troubleshoot your model
It sounds like your model has/had some elements that referenced other elements of the model. It is possible that these “other elements” were deleted.
For example, maybe an interior wall was set adjacent to a space, but then that space got deleted. Another example might be a system that had been specified to receive outside air from another system, but then the other system was deleted. This may be the case if you were using an ERV or supply fans to provide outside air to the space conditioning systems. There may be other cases like this that I am not aware of involving other elements like overhangs, sidefins, etc. The point is that when you delete something that is referenced, sometimes the reference will remain, but the reference will point to nothing (since the object has been deleted) causing an error in the program.