I had the same issue and its a stupid bug based on the cloud save mechanics. This bug happens if you have a lot of save games in your save game folder. A save game took like 5 to 8 MB which is quite a lot. Once you have to many save games the cloud storage of steam is full and it will not sync all save games and options anymore. The save games are that big because they save a huge screenshot of the current game into the save game file.

You can easily solve this issues:

• Move to C:\Users\<username>\Documents\CnCRemastered\Save
• Copy or cut all your savegame to a new folder on your desktop (just to save them into an other location for recovery)
• Delete all save games in:
  C:\Users\<username>\Documents\CnCRemastered\Save
• Start the game. All campaign progress and options should be saved now.

Command & Conquer Remastered save game location:

• Default save game location: 
  C:\Users\<username>\Documents\CnCRemastered\Save
• Save game location if you using OneDrive: 
  C:\Users\<username>\OneDrive\Documents\CAndCSaveGames