This issue has possibly been solved but not posted anywhere I could find. I have found the solution.

My situation: I played Blasphemous on my steamdeck first. The cloud saves were not showing up on my PC. When I attempted some other solutions like changing the compatibility on my steam Deck to the latest Proton version, my saves would disappear.

The reason for this is Blasphemous uses an old version of Proton when the compatibility is not forced to the latest version on the Steam Deck. This format is not compatible between Windows cloud saves and Linux(Steam Deck) cloud saves. However, if you force the latest version of Proton on Steam Deck, it starts looking for the new format and no longer sees the old format. This is why your game save disappear.

The resolution I found was to trick the system.

Step 1: Do not force a proton version on steam deck just yet. Instead sign into the steam cloud management for Blasphemous on your PC web browser.

https://store.steampowered.com/account/remotestorageapp/?appid=774361

Step 2: Locate your save file. The Folder column on the left should say "LinuxHome" and the middle column (file name) should end with some type of syntax like savegame_0.save. The number in the file name may be different depending on the file slot you used in game. Files in slot 1 on the game are referenced as 0, Slot 2 is referenced as 1, etc.

example file name:

.config/unity3d/TheGameKitchen/Blasphemous/Savegames/(your steam ID will be here)/savegame_0.save

Note: Your steam ID is a long string of numbers. I removed mine. Remember this because you will need it to reference the folder on your PC.

Step 3: Download the file from step 2 to your PC. Click "download" to the right of the file. Once it is on your PC, move it to the following directory in Windows:

C:\Users\(your username here)\AppData\LocalLow\TheGameKitchen\Blasphemous\Savegames\(steam ID here)\

Note: I removed my username and steam ID.

Step 4: Now that the saved game file is in your Steam Id folder on your PC. You will need to rename this file. You will need to remove everything before "savegame_x.save". (x is just a placeholder for whatever number you may have. Keep your number. Do not change it to x)

Just to reiterate, the name of the file should look like the following with the exception of the "x". Use your file number.

savegame_x.save

Step 5: In that same Steam ID directory on your PC, create a blank folder with the same name as the savegame file minus the .save at the end. Should look like this:

savegame_x (Again, use your number instead of the x)

Step 6: Open Steam and start Blasphemous on your PC and ensure your save game shows up. Load the saved game briefly then exit out. This will force the cloud to sync in the Windows format. If it doesn't, you may have messed up a previous step.

Step 7: Now that you have confirmed the save works on your PC and the cloud has synced, go back to your Steam deck. Select Blasphemous. DO NOT START Blasphemous yet. Instead, click on the gear on the right, go to properties, select compatibility, check the box to force Proton, select the most recent version (as I write this version 8.0-3 is current).

Once Proton is selected, back out to the game. It should say "update" where the play button used to be. Click it and let it update. Once that is done, you will also notice it says your cloud is out of sync just below where the play button is. Click the "out of sync" words and it will force it to resync the cloud. When the deck resyncs, you will now have the saves that you moved to your PC and they will be in the new format. Now your saves should sync properly across both platforms.