I've got a large assembly with inadvisable organization. We've done this to ourselves, and it is known now to simply be a self-inflicted pain in the workflow. I cannot share the file.
In the assembly view, there are no rebuild errors, no error symbols, with everything resolved. In the configuration list, that configuration still has the yellow triangle [!] symbol. I am trying now to remove errors, and may just have to ignore this one.
I also realize that this is an annoyingly vague question for a big thing so overworked, indeterminate, and complicated. It could be mates, fixed items, virtual components with sketch relations to other components, or something other I haven't considered. I will share and respond to relevant questions as able. Thanks.