I've noticed that in all of the KNIME chemoinformatics stuff, the only thing that exists that removes fragments is the RDKit Salt Stripper. Whilst I've found this useful, it does require you to define salts when the pre-defined ones are not wanted.
A simple node that removes the smallest fragment (or keeps the largest fragment) in a "molecule" would be great. I'm somewhat surprised this hasn't been implemented in one of the APIs before (though I post this in the CDK library as I rely on CDK slightly more than the other 2).