Yes, they will, but just make sure to save the OOBs you've modified in the custom OOB folder or somewhere else, and you'll have the changes you've made and can copy them over when V3 comes out.
Please read the GG section on the "manage OOB sets" function of the GameOptions programme, which is there to deal with/manage user mods and/or restore oficial-issue sets e.g for PBEM.
"Running WinSPMBT" link in the GG - then scroll down a bit.