There may be conflicts between mods and research features. Mods can override or change default behavior leading to bugs.
Shield Harmonics is an end of tree tech called a "capstone"
Capstone techs can be researched over and over they do not "stack".
You get the "perks" of a capstone tech when you research it, however if you research a deferent tech or a different Capstone you loss the perk of the one you already researched.
It is the way the game is designed and is neither broke nor bugged.
This losing the already researched perk is while as designed IMHO a design mistake but has not been seriously discussed in this or the steam or discord forums.
The lack of Shield Harmonics being labeled as a Capstone and the lack of a popup explaining what Capstones are has been logged for the Developers to look into.
Gypsy 2299 AKA Ghost 88 on Steam and Discord