You have a couple of ways to proceed here, but Shelxpro suggests you
take the update route, using option [U].
This will take the .pdb file that you've output after spending countless hours working on in O, and convert it to a .ins file.
If you only want to update a couple of residues, make sure you remember which ones those were...it'll ask you.
Next, you'll be taken through every residue that has an occupancy other than 1.0, unless you tell it to skip the rest. Beware! O doesn't recognize free variables, so if you have used FVAR to define occupancies for a residue or alternate conformations, or for thermal parameters, you need to go into the new .ins file when you're done and put the FVARs back.
You can also have it check your waters to see if there are any occupancies that need to be halved.
If you have hydrogen atoms, all of your AFIX restraints will be lost and you'll have to reintroduce hydrogen atoms using HFIX in your new .ins file, just as when you first added them.
If you have alternate conformations, they will be entered into the atom list with the offset that was applied in order to get them into O (HELP7). As such, you need to go through to each and every one in your new .ins file and change them back to the PART format (HELP3).
If you have gone to anisotropic thermal parameters, they will be lost in when you output a .pdb file from O. So, you need to at ANIS to the instructions in your new .ins file.
It's pretty labor intensive, but this is the only way to do this I'm afraid. Don't worry, you'll get used to it.