Hi @fvalbores! Thanks for the detailed summary!
The ability to provide a SampleData[PairedEndSequencesWithQuality] as input to quality-filter q-score was added in QIIME 2 2017.12 - this error is consistent with trying to provide this type of input with an older version of QIIME 2. You should be able to upgrade to the latest version of QIIME 2 and attempt to re-run quality-filter q-score (you shouldn't need to reimport your data) with your paired-end reads.
Let us know if that works for you! Thanks! 