How to upgrade agents from sp2 to sp3

Hello

LDMS 9.0.3.1

We have upgraded to SP3, however ee have 2 sites who collect the .scn files locally and we then copy the .scn files manually to the core server. 

These are still using the SP2 agent which is cauing problems with software identification.

Please can anyone advice what will be the best way to upgrade these agents as they do not connect directly to the core server.

Thanks, Tom