Unfortunately, Qiime 2 does not have a built-in method for dealing with these. 
https://github.com/qiime2/q2-cutadapt/issues/11
You can deal with these outside of QIime then import, but I might be outside the scope of your question. There is some more advice over here:
May I ask how you came in position of mixed-origination reads? Most Illumina reads are one way.
Colin