I'm not sure if you've hit a bug or you may have done things in the wrong order.
What I normally do when unlocking an Engineer and wanting to do an upgrade, let's say Farseer and the FSD, is to first do all of the FSD upgrades with Farseer up to level 5, and then I can use the pinned blueprint up to level 5 remotely.
Also remember you cannot apply an experimental effect remotely, you have to get the engineer to do that.
What I would do in your situation, is to remove the modification on the FSD, and then apply all the upgrades again at Farseer. Whilst it sucks that you will have wasted your time and materials, that might be the only way and you will have to treat this as a learning experience.
This is probably the way to go at least I’ll be able to figure out how it works that way, what’s a few more hours gathering lol .... I guess I just really got a bit offended , I like the game a lot ( my Wife says I like it Too much ) and I really misled for the first time made me take it a bit to personal lol
I really appreciate all the great advice