When I error with uploading in Eclipse, I uploaded file using Command prompt. See details in this site. The following is the implementation in my computer.
First of all, adding java path in Edit System Variable through System properties >> Advanced >> Environment Variables >> Edit
It is not needed earlier as I use Eclipse IDE.

Then, open command prompt and locate appengine sdk path. At the same time, I copied war file of my project under bin folder. Be sure that the file is currently clean.

Then write >> appcfg.cmd update war

Then, type your gmail and password to your GAE. Then file is uploaded if password is correct. If it happen failure upload, clean your app file. Test it now. But sometimes it happen error in GAE, if so upload again. Changing version may be worked.

Reference : Uploading Your Application