Thanks for all the great info @jbethany!
Not really related to your issue here, but we actually support this kind of filtering directly in QIIME 2! There are a few examples floating around the forum, but this one is a good starting point! Apologies if you already knew about this, but I wanted to toss it out there --- I had actually been assuming you performed your filtering in QIIME 2, which was why I asked for the filtered feature table's provenance --- I would've been able to see exactly how filtering took place. No big deal, but provenance is certainly one of my favorite features of QIIME 2! 
The metadata file you attached doesn't have a Combo column 
, can you please share the exact command you ran (since it doesn't look like your old command would've made sense here), as well as the exact error message with it?
Also just for grins, does it work for any metadata column?
Thanks for your patience!
PS - There are no "required columns" in metadata - you don't need to include things like BarcodeSequence or LinkerPrimerSequence if they aren't applicable to your study! Also, you can name the ID column whatever you want, so if you would rather it say Sample (instead of #SampleID, which is a QIIME 1 compatibility thing), you are more than welcome to change. No worries either way, just wanted to let you know! 