One thing to check and make sure that those part are in same location.
Are there multiple files of the same part number saved in different locations???
What's the error message reporting? Can you have both of the subassemblies open at the same time (it was not clear to me in your post).
If you RMB on the parts with the error, what is the error message?
This is where you need to start. Without that error message on here it will be very hard for anyone to answer your question.
The causes for these issues are vast and we can all guess as to why it is happening, the software is pretty intuitive I am guessing there are 2 different file locations for the same part as mentioned above by John & Deepak.