Hi @Danyl_McLauchlan,
Great question. I know some folks with mixed-orientation barcoded reads use this tool to extract the barcodes and orient the reads prior to importing to QIIME 2 (possibly by doing two passes through this tool? I have not looked): GitHub - najoshi/sabre
However, since you have combinatorial dual-indexed reads that complicates matters, so I'm not sure if sabre will cover your needs but it's worth a look.
If any of the qiime1 virtual machines are still around, you may be able to download and use one to access extract_reads.py...
this is functionality that is long-overdue to get into QIIME 2 but since combinatorial dual-index reads (with/without mixed orientation) represent a small fraction of users' data (that's been reported on the forum at least!) this has not been a very high priority... any volunteers??? I will be curious to hear what tools others are using to prep these data, since those could be wrapped in QIIME 2 to make a seamless workflow.