Hi Catlin,
I have ask the mixed orientation data problem before and Nicholas helped me to solved my problem. Please check the bottom part of this thread
In my case, based on the taxonomy data using the mixed orientation data, I know which samples are corrected and which samples are in the reverse orientation. So I used vsearch --fastx_revcomp command in the Vsearch to correct those samples and move them to Qiime2 again.
Hope these steps also work for you.