Just skimmed this quick, but question. Did you direct windows to the alternate drive via "MOVE TO" ... if not or if you dont have those options in your right click menu, add them with AddMoveTo.regAddCopyTo.reg then go to c:\\users\[username] scroll down to SAVED GAMES dont move the dcs folder, move the parent folder SAVED GAMES, right click on SAVED GAMES, select MOVE TO, select the drive where you want it to go and save.
If you've already moved the DCS folder, simply leave it where it is and follow the above instruction, moving the empty saved games folder to the folder you moved the DCS folder to, then highlight the DCS folder and drag it into the saved games folder. All should be well with the windows issue after that