So after some trial and error i found out when the problem occurs.. it appears that when steam/homeworld copies the .big file from the workshop folder into the dataworshopmods folder that for some reason the .big file is corrupted.. so its a VERY simple fix instead of what i wrote earlier..

Go to

C:\Program Files (x86)\Steam\steamapps\workshop\content\******\759628723 (****** is the workshop given number of hwrm)

find the mod file STCR.big and copy it to

C:\Program Files (x86)\Steam\steamapps\common\Homeworld\HomeworldRM\DataWorkshopMODs\76561198042323876\759628723 (there should be a STCR.big file in one of the last folders, this is what your are overwriting)

Overwriting the .big in there.. then you should be good to go :) though following any updates these steps might be required again

Hope this helps :)
This is SO much easier and quicker than the unsub delete folders resub method I was using