Your post is not very easy to understand; what does "For a lot of atom types, the new file did not define" mean? It is often better to show actual input/output instead of trying to describe what is going on.

Topology and paramter files come in pairs which should be used together. Furthermore a PSF generated with a given RTF/PARAM file pair should always be used with this same RTF/PARAM file pair.

Your two main options are (very briefly):
1. Keep using your old RTF/PARAM/PSF files. Best choice if you want to continue an ongoing project.
2. Regenerate the PSF with the new RTF/PARAM files and use this combination instead. Best choice for new projects. I have no idea how old your old version is, but the organization of the toppar directory may be different in the new version. Look in the toppar/stream directory, and you may find the missing bits and pieces there.

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden