I have found some strange behaviour in LabVIEW 2015 SP1 regarding TDMS files. I discovered that a group in a TDMS file that has properties but no channels cannot be deleted when it is the last group in the file.
In order to demonstrate, find the attached demonstration VI.
When I first delete the group without data (A) and then the group with data (B), everything is fine.
When reversed, thus the last group in the TDMS file has no data / channels, it cannot be deleted.
