I’ve got a little over 200G of samples and loops I’ve collected over the years and mixed in there are a bunch SDII files. I’m worried about the future compatibility of these so I’d like to batch convert them to AIFF or WAV. Is there a way to scan these large folders and convert theses items in place, replacing the originals? I can’t think of another reasonable way to do it.
I wouldn't do that. I'd keep them as SDII files and convert them as needed. SDII as a format will live for at least another 20 years or longer, too many important Pro Tools projects use them.
Going from SDII to WAV or AIFF is tricky because SDII files carry embedded metadata that it not 1:1 supported in other formats. The audio itself will convert perfectly, but the embedded metadata is often very important.
My official advice is don't worry about converting them, when you use them in a project, convert them then. 200G is a lot of files and you have no way to tell if anything went wrong in the process because you can't inspect 200G files in one lifetime, so you will be flying blind.