I have the same problem (for ax 2009 version)
What that is reflected on Ax (mainly webcontrols) - no problem, since I run at last axupdateportal.exe
What is not reflected - since everything is webpart, I am seeking for a way to put things on axwebparts.cab (didn't find any way yet, but it is reasonable that exporting all the webparts, decompress axwebparts.cab, merge it with the exported files and compress axwebparts.cab again and doing :double click, import the new compressed cab will solve it).
Let me know if you find any solution, since either do I need a solution for that.