Like I said before, cutadapt won't change your quality scores, and neither will importing. I am 99% sure that the FastQC report is misleading you:
- FastQC plot is showing you ~58 histograms
qiime demux summarizeis showing you ~245 histograms
I'm not sure how, but the FastQC plot is grouping many of the bases in the plot together, which I think is a bit misleading.
One option, if you really want to convince yourself, is to import your multiplexed reads into QIIME 2 using a manifest format (which assumes reads are demuxed). Doing this you would basically just have one sample. Then, you could run that imported Artifact through this viz - you should see something very similar to what you are seeing post-cutadapt.
Finally, if you want to share a private link to your data, I am happy to take a look for you.