Normally, the game's interface prevents a player from removing/changing ship's equipment if there is a mod installed. The ship's available equipment is greyed-out/locked in the upgrade/repair interface. But if one selects the "Minimum Preset", this will remove/swap all equipment from the ship, including the modded one.
I have a save demonstrating a Phoenix (TOM-189) that initially had some green mod somewhere (I can not remember where exactly -- it was a rare boarded NPC ship having a mod pre-installed), but now it does not. The mod section does not list any mods, but also it does not state "No modifications installed" and upon sell attempt there is a warning about selling a modded ship.
I also have a pair of gifted Chthonios nearby still sporting shield/engine mods. Feel free to test it out.
