What steps have you taken prior to this? Simply deleting a symbol from DxDesigner and re-running packager should not give you this error, it will just delete the surplus capacitor from the PCB design. The existing reference designators will be retained. For packager you need the 'Package Symbols' option, and 'Only Extract Missing Library Data' if you've not updated anything in the library. The 'Repackage' option will re-assign reference designators which you probably don't want to do. The other option is to just pull the changes into Expedition by clicking on the first 'amber LED' in the bottom right hand corner of the Expedition window, this will re-run packager with your previous options.
Thank you very much for your response. Now I can properly synchronize schematic and layout. I think the problem was that instead "Package Symbols" I run the "Repackage". Now everything works fine.
I have also another question to you: when I do the ForwardAnnotation in Expedition PCB I get a lot of such warnings:
Symbol / PartsDB property mismatch:
Resolved PartNumber = CAP_CER_NEW
Symbol Property: Description = Ceramic Capacitor, X5R
PartsDB Property: Description =
How can I solve that problem? I assume that somehow I have to copy desription property from central library to PartsDB database, am I right?