Hi @Martin,
Thanks for posting! To be clear, the presence of the linkerprimer is not a problem (when denoising with dada2 you can just set the --p-trim-left parameter to equal the length of the linkerprimer to remove it); however, the presence of the barcode is.
In a future release of QIIME 2 we plan to add support for extracting barcodes from reads in the way that you describe; for now, you will need to use extract_barcodes.py (a qiime1 command) or other external scripts to extract the barcodes into a new fastq file before importing to QIIME 2.
The good news is that once that barcode extraction occurs you will have separate forward read and barcode read fastq files, which can then be imported and processed using the EMP protocols!
I hope that helps! Let us know if you still have trouble after extracting barcodes.