GUPs are storing either full definition files ("full.zip") or delta files. Both have to be created by SEPM. GUPs can only be updated by SEPMs.
The content of the SEP client which is carrying the GUP is independent of the GUP content.
BTW, every time the SEP client (smc.exe) will be stopped the SharedUpdates folder will be flushed. Your GUP should run 24/7 to prevent this.