Hollow Knight developer Team Cherry has announced that an update due to go live on Monday, August 15th will bring a much needed change to the saving system.

Mentioned in a Steam post, the developer said "Soon we'll be making some changes in order to support cross-platform cloud saves between Windows, MacOS, and Linux (including the Steam Deck)!" with the plan for it to go live on Monday at 5AM UTC. There's a few important notes they also included:

If you wish to make a backup of your save here's the locations:

Not mentioned in their post, but there is currently a rare issue where the graphics might glitch-out completely. To get around this, you can set the game into OpenGL mode by setting this in the game launch options in the Properties of the game in your Steam Library: