How to save/overwrite an annotated file with Evince?

Use recent version of Evince, no need for workaround.

I need to click through the folder to find the pdf location manually because the saving location is not the original pdf location by default.

The said issue is apparent for Evince 3.10.3 in 14.04 release. In my case, the default path is $HOME/Downloads rather than $HOME/Desktop. Not sure why the difference.

With recent version of Evince, the said issue is non-existent. I have at least confirmed that saving location is same as the original PDF location by default, using Evince 3.18.2 in 16.04 release.

I have the feeling there should be an easier work-flow. Do you have an idea?

Sure. If you are consistently working from particular directory, consider to add that directory to the Bookmarks in File Manager. This way, you can always select the directory from the sidebar in File Chooser Dialog. This will reduce to just one or two clicks. Good enough?