The Launcher marks all of my STEAM Workshop, not local mods, as corrupted whenever I restart my computer. The mod files are still within the Arma 3 folder(Steam\steamapps\common\Arma 3\), untouched.

The only way to fix it is to go into the Arma 3 folder and manually delete the affected mods and restart Arma 3, in which the launcher still has the mods corrupted, and goes through the check, finding no folder, and Steam will then individually redownload all of the mods.