Merging all waves in sub folders

I think you problem calls for recursively searching all folders/subfolders from a specific starting point while extracting a list of waves, and then finally concatenating this list of waves. There is a very old thread about listing all waves, which should get you most of the way there. The concatenating part is trivial as long as you don't have to fight with different wave sizes. See here:

https://www.wavemetrics.com/forum/general/get-list-all-loaded-waves

The function from this link might be a bit overkill, since it covers all cases you'd ever want. Maybe trim this down to your specific case if necessary (i.e., only recursively listing waves).

The files are loaded as hdf5 files and import about 300-500 waves, but the data group gets loaded with each individual wave in a separate folder.

That should happen only if each dataset is in a separate HDF5 group.

Alternatively, with the hdf5 loader, I would prefer to load all waves into a single folder, but there doesn't seem to be an option to do this either unless you select each of the 300-500 individual datasets and load them as a dataset instead of a group.

If you can post a sample HDF5 file, I will see if I can figure out how to do this programmatically.