It was probably the caching that got me. Partial updates works now. Cooks was probably too fast for me to even notice when it just read the cache. So why is it using the cache this way?
PDG's caching system is based on files. The Automatic caching mode means that if the expected output files are found on disk, then the work item will cook from the cache file. Write Files means it always overwrites the cache files on disk, and Read Files means it fails if there's no cache file to read. We've been making some improvements though, including more consistent behavior when upstream work items are modified (see details here: https://www.sidefx.com/forum/topic/73032/
Dirtying cache files when attributes are modified upstream is technically possible as well, but may not always be the desired behavior. To do that properly PDG would need to track each of the attributes actually used by a work item, not just the ones that it actually has. Some attributes are just copied through the work item from their parent and then used later downstream. For example, the first node in the graph might be an attribute create or wedge used for configuration purposes, or something that loads a configuration file from disk.
As the topgeometry is not working, is there a way to get the geometry back in a similar fashion when using the top network? Should I for-loop a file node?
You can use a SOP for loop to load in the files, or you could also try using the File Merge SOP. That's mainly used for loading in distribute sim slices, but if you're writing out a sequence of files with consecutive numbers in the name, it can be easier to use than a loop.
I'm looking into the TOP Geometry issue you logged, although I'm unable to reproduce the crash on my end at the moment.