Sounds like a Parent/Child issue.
The drawing has to contain all of the items you would like to update or check-in and they will do so. I do not know how to attach a drawing to an assembly, I think it's the other way around.
Check in from the assembly ... No drawing present.
Check in from the drawing ... All model items and assembly present.
Checking in from the drawing would work but I need to check in a higher level assembly that uses this sub-assembly. When I check that assembly in, this sub-assembly drawing doesn't get included in the mass check-in.
When I check in an assembly in other cases it works fine and brings the drawing along (when the drawing doesn't have multiple references):
It seems like the multiple references is a bug and messes up the assembly->drawing link while checking in/out.
Still haven't gotten an answer so I made a simple dummy assembly and took a few screenshots to illustrate the core problem.
I have a top level assembly. Inside there's a sub-assembly. I made a drawing for this sub-assembly. When I check in the top level assembly, everything comes with it as expected.
Check in top level assembly. Sub-assembly drawing (in blue) automatically included. All good.
Next, I change my sub-assembly drawing so that one of the views references a part in the sub-assembly, rather than the sub-assembly itself. If I go to File->Open and click on References for the drawing, I see that it now has multiple references (since one of the views references the part):
Now if I try to check in the top level assembly as before, the sub-assembly drawing is not automatically included!
The only fix I have for this right now is to make a separate configuration in the sub-assembly every time I want a drawing view that references an individual part. That way, we avoid the multiple references. This pollutes the number of configurations needlessly, especially if I want to reference multiple parts in an assembly drawing.