In the 2019.10 release a bug was “fixed” in Qiime2 studio - " fixed a bug that prevented
MetadataColumn values from being decoded properly - this was mostly an issue for q2studio". I have just had a chance to look at this fix, using the latest version of Q2S and while the initial metadata collapse seems to have been fixed and the appropriate feature table is produced, downstream analysis of this table i.e. to plot taxa is not possible.
It seems as if the command is looking for the collapsed metadata groups to appear in the Sample ID column -
raise ValueError(‘Sample IDs found in the table are missing in the ’
Hopefully not just an error on my part.