Thanks for your reply Kelvin but my Link to property dialog box doesn't look like that. I have no option for model found here. The only options I have are current document, Model in view to which the annotation is attached (which is grayed out) Model in view specified in sheet properties, and Component to which the annotation is attached. I also have only one drop down box as well. I'm On SW 2105.
you do want the "view specified in the sheet properties" option, then double check the sheet properties for each sheet, and make sure it is specifying a view of the desired configuration.
Is the number completely different or are you adding a prefix or suffix to the file name, if you're adding anything to the file name then I would create another custom property that would pull that prefix/suffix and add it inline with the part number/file name, the note would be stacked...
Then in the drawing file you would have your linked note like this
or something along those lines.
Then in your Custom Property Tab Builder you would add the A, B, C designation by using the Configuration Specific Tab ...
There are possibly other and better ways, but this is where I would have started from.