Using Kubuntu 16.04 flatpak Gimp 2.10.4
Confirm that any extra files required by plugins need to be reinstalled when the runtime(s) are updated. Not difficult if the required files are archived somewhere, ready to copy over. example: https://i.imgur.com/XLHUsG1.jpg Common sense here and do not overwrite any of the existing runtime files.
31 files for just bimp(18) FFT gimp-lqr-plugin gmic_gimp_gtk(2.2.4) nufraw-gimp(0.42)
Second that suggestion.