Hi @ylor!
Congrats, you found a bug! 
I opened an issue for tracking a fix for this.
The good news is that you have some other options available to you!
The CASAVA 1.8 format expects demuxed reads to have filenames that look like this:
L2S357_15_L001_R1_001.fastq.gz
The underscore-separated fields in this file name are the sample identifier, the barcode sequence or a barcode identifier, the lane number, the read number, and the set number.
The CasavaOneEightLanelessPerSampleDirFmt is a variant of that format that we have seen floating around, it is the exact same as CASAVA 1.8, except it is missing the lane in the filename:
L2S357_15_R1_001.fastq.gz
Check out the fastq manifest format, you should be able to create a manifest for these files and import!
Just curious, how did you stumble across the CasavaOneEightLanelessPerSampleDirFmt format? We haven't really documented it or advertised it, which is why there isn't much info floating around about it. Anyway, thanks, and keep us posted! 