I have seem to found a solution to my problem. I go to the CC workshop page, hover over the mods, there is a little box with a + sign in it, click on it, then start up the game. Upon game start up it will take a few moments to install the mod. I did this in bulks of 10 and did it maybe a total of 5 times. Seems to have installed most if not all the mods I wanted.

ALSO; when doing this method you may accidentially disable previously installed mods, but it will not uninstall them, or delete them from the CC directory. It will add .disabled to the mod file in your CC directory. To get around this issue simple go to the CC directory and delete the .disabled.

For example, change

w40k.rte.disabled

to

w40k.rte

I got a similar problem i have like almost all the mods in the workshop and after maybe 2-3 days

the workshop likes to unsubrcribe to 2 or 4 mods so my Void Wanderes save fiile is brocken and i have to click subscribe boot up the game do that 3 times and it all magicly fixes it self but OFCOURSE it has to download EVERYTHING again and with that many mods it gets boring have to wait to download exract and load.

Any help

Well if you go to your Cortex Command directory (mine is C:\Program Files (x86)\Steam\SteamApps\common\Cortex Command) it shouldn't actually delete the .rar file or the extracted .rar. It seems instead of deleting, CC renames the files upon startup. For example, it will rename the folder voidwanderers.rte to voidwanderers.rte.disabled. You can simply rename the folder back to voidwanderers.rte. I think when the game starts up and has that waiting period it is either renaming files or unpacking them from the .rar. If you have the program Winrar you can even unpack the files yourself. My .rar files are stored in C:\Program Files (x86)\Steam\SteamApps\common\Cortex Command\WorkshopMods.

when i got to the folder every single mod had the main file the mod.disable file so i have 2 files from every mod do i need to delete EVERYTHING with a Disable near it?