Try copying the code into a local file on your computer, like this:

1. Use the Copy tool to copy your code to the clipboard. The amount of memory reserved for the clipboard is pretty big, so it should copy everything.

2. Paste it into your text editor of choice after making a new file.

3. Save the file with the correct file extension and you are done!

I am having a similar issue with a PJS. Just for anyone who answers this thread to know.

Since no one has provided a work around or fix yet, I suggest using "Report a Problem" to get help directly from Khan Academy staff.

Hi everyone!

Would anyone be able to provide some links to projects that you aren't able to save? I wasn't able to reproduce this issue on my end so some specific examples would be helpful.

Thanks!

This is the link to a copy of the project which wouldn't save either. The original copy is on another account that is my younger brother's. He and I were working on it together. 
Note: I had no issue saving the project before so I am under little suspicion that the problem has anything to do with the project. Perhaps my internet?
https://www.khanacademy.org/computer-programming/new-program/6613060216274944 

Thanks Peregrine! I was able to reproduce that issue and have submitted it to the team.

I'm thinking it has something to do with large projects, because other smaller projects appear to be saving just fine for me. If anyone has examples of smaller projects not saving, please share the links!

I had this issue with a project of mine. I had lots of fills and rects in my program, and at a certain point it would not get saved. So instead, I made an array of data and a for that would turn the data into rects and fills.

Since maybe it won't save because of the timeout, maybe you can try to add a button to cancel the saving instead of their being a time until the saving completely cancels it.