There are two versions of the PEP software, version 1 and version 2. Although you probably used PEPv1 to convert your config, you should use PEPv2 to update it.
Assuming you are using PEPv2:
1) Can I have multiple projects open at the same time as I rebuild in color?
No, but you can merge the old and configs together whilst you edit the new one.
2) Is the correct way to store codes on the component page? And can I delete the Codes pages I have?
No, you should use the database as discussed in the manual.
