Unfortunately your instructions did not resolve the issue. I noticed that under "Icons & Cursors" -> "Folders" the icons for "Live Folder (Back)", "Live Folder (Front)", and "Live Folder (Data)" (along with a few others, were blank. I tried Restoring default icon but they did not change. I then went to manually change them and was presented with the correct icon already selected. This allowed me to restore them in this section, however they are still displaying incorrectly in explorer. I've rebuilt the cache, repaired images, and fixed the shell icons for all processes once more to no avail. Also if it's relevant the image shown under "Look & Feel" -> "Live Folders" shows contents only; the front and backs of the folders are invisible. Changing the theme here changes the preview image however selecting the Windows Default Icon set takes them back to invisible.

I already did an sfc run. Not 100% sure what did it, but things seem to be back to normal now. Not sure if it just needed an extra restart or something but all is good now. I wish I could isolate the specific solution to help others in the future but somehow a combination of all suggestions above and a fair few restarts managed to fix things. Thanks for your help guys.