I don't know why it's doing that, but I'll try to help. I see two options (there may be others).
1. Create a second configuration of the main assembly. Have one with this sub-assembly suppressed, and the other with the conflicting component(s) suppressed. Then use the correct configuration in the drawing.
2. Pack and Go the assembly to another location, along with all it's dependent files. Save this for your other project. Delete the offending sub-assembly in your original main assembly.