You use FileMaker Server, isn't it?
Because in FM Pro there is nothing to upload - existing file is opened with FM Pro 10
I'm guessing that the updated file either has a different filename or is located in a different folder than the original.
Open Manage | External Data Sources...
Search through all the entries here for any that still refer to your original file by name or folder location.
Update them to refer to your new file and the issue should be resolved.
If your solution is now an all in one file solution, you'll probably want to use Manage | Database | Relationships to point each TableOccurrence (Double click each box in question) to the correct table in your new file and then update all scripted references to do the same as well.
FMP advanced's Database Design Report can be very useful for cleaning up old data source references.