If this is the same issue I had, you could replace the N:0:1 to match across your forward, reverse, and barcode gzip/fastq files. The command would be to change the N:0:1 to match all.
The problem also occurred from our sequencing core where the forward would have the barcode N:0:1, but everything would be sequential (barcode file N:0:2) and reverse N:0:3.
A unix command to search and replace all N:0:2 and N:0:3 across the files to change to N:0:1 allowed me to import correctly. Of course, your problem may be different and before doing this, make a copy of everything and don’t use.
I’m at a different station, will provide the unix commands when I get back. Ben