Hi Derek,
You might want to look at this thread for pointers about upgrading Bio-Formats. If you don't use containerized deployment, the second solution might not be applicable and you might have to replace the JARs if you want to upgrade Bio-Formats on the server.
Thinking more about your situation, it might be worth trying to upgrade Bio-Formats client-side only first. The DICOM fixes in Bio-Formats 6 might be sufficient to upload filesets without cross-folder detection.
The workaround you described in your last post might be sufficient to get you going until OMERO 5.5 is released.
Best,
Sebastien
