I think you might have to write the soulbonding one, to make it go away ;-). Perhaps an AU where the memory chip was an experimental variant on the Jeeves thing they do on Jackson's Whole, or the telepathy thing, to make Illyan a perfectly loyal soldier because he is so psychically connected to his Emperor. Only it doesn't work like that and Illyan ends up trapped and bonded to a dying Emperor, fated to go through Ezar's final illness with him and die with him, until Aral and Cordelia come up with a way to save him which leaves him sort of half-bonded to Aral.... IDK, I'm a bit sleep-deprived right now, you can probably come up with a better plot.

I think the post-Memory adjusting to not having the chip is wide open for fic, really. The time thing makes a lot of sense. There must be so many things that he hasn't had to do for thirty years, all showing up at once to bite him.