In case you wanna use it, a while ago I came up with a way to make Unity not lose save data stored in PlayerPrefs when you update a web game. Source code is at https://3p0ch.newgrounds.com/news/post/1086279 You'll make everyone lose their data when you push an update implementing this for the first time, but then all future updates won't lose everyone's save data.
Sounds like it should work, and if you think you might change the structure of your save files in the future and would rather just have to change the normal save files (for a desktop/console export) and not worry about also changing how PlayerPrefs saves the data then that approach might be less work in the long run. Just be sure to either ensure backward compatibility, or change the idbfs subdirectory if you do make any changes that break backward compatibility and you actually want to lose the old data.
On the other hand, if you don't think you'll need to mess with the code for save file structures, it might be easier to just pop in the class to override PlayerPrefs for HTML5 exports and be done with it.
Yeah, it’s much easier not doing any PlayerPrefs stuff at all!
I think I have something. It was a little bit more complicated but, after doing some voodoo mentioned in the comments, it seems to work! Survived me making a couple of new builds at least.
Of course the next public build will kill existing webgl saves, but it would have done that anyway... Sad times. Thanks for your help!