Hi @Sara_Jeanne08,
My understanding was that you have already demultiplexed these with QIIME1's split_libraries_fastq.py, which already performs the same quality filter as quality-filter. If so, you can proceed directly to deblur (but if you've already passed your data through quality-filter that's fine too.
I just mentioned the q2-quality-filter plugin in case you want to replicate these steps in the future when QIIME2 supports methods for dual-index paired-end reads and QIIME1 is no longer needed for your analysis.
Not to worry — I think that text really just means that unjoined paired-end reads are not supported. If it's any reassurance, the community tutorial for processing paired-end reads recommends deblur for denoising joined paired-end reads. If you do get an error then perhaps I have misunderstood the format that your data are in, but as far as I can tell you should be fine.
I hope that clarifies!