I recently switched from manual download to downloading it with the itch app, for some reason it reset the projectile speed upgrade but nothing else.
I have 0 explanation how that could even happen, but it did.
Do you mean that you switched from the PC/Android version to the browser version? Unfortunately, cross-platform saves are not supported right now.
WEB version saves are stored in the browser cache and progress is saved only for a specific browser. From this point of view, the most stable version is for PC and Android.