I got the following error on uploading my project

 "There was a problem loading your project:

Too many files in zip (1869 > 1000)

Please try deleting the ZIP file and uploading another one."

I would not be able to delete files to reach the 1000 limit without losing content of the game.

I read that maybe it is possible to have this restriction lifted, would this be possible?

No, this particular restriction is non-negotiable, sorry. That's a web game, right? Please offer it for download instead, with just a small demo for online play.