I first want to note that my suggestion here is going to be making the assumption that you have a
FeatureData[Sequence] artifact (which is very common - but please let me know if that is not the case, because this recommendation won't be possible without it).
With that being said, if you do have a
FeatureData[Sequence] artifact with the "complete" set of features in it, then you can filter that file down using your filtered table. More information on this method can be found by entering
qiime feature-table filter-seqs --help, just for your reference.
From here, you can use the output file from the above command (which will also be a
FeatureData[Sequence] artifact) as the input for
qiime tools export, which will allow you to export this data in FASTA format. More information on the parameters for this command can be found by entering
qiime tools export --help, or checking out this tutorial.