I remember a long time ago being told that Mulder's abduction was not part of the original plot of The X Files and only happened due to financial negotiations going wrong between David Duchovny and the producers. Was this really the case?
tl dr - I believe you could consider this partially correct.
In the Season 7 Wikipedia article, it states:
Before the season aired, David Duchovny filed a lawsuit against 20th Century Fox. Duchovny was upset because, he claimed, that Fox had undersold the rights to its own affiliates, thereby costing him huge sums of money. Originally, in the contract, Duchovny was eligible for an estimated five percent, but, according to him, he "had seen only a fraction" of the money. Eventually, the lawsuit was settled, and Duchovny was awarded a settlement of about $20 million. The lawsuit put strain on Duchovny's professional relationships. Although his lawsuit never called Chris Carter a defendant, their friendship was notably impacted. One anonymous source noted that "the whole lawsuit thing revealed that Carter knew (Duchovny) was getting screwed and didn't warn him. Carter proved where his loyalties lay with his actions."
According to the BBC:
Duchovny had only appeared in a handful of episodes of the current series after a legal battle with the network over payment.
NOTE: The term "the current series" refers to season 8.
In this note on a fan based website stated:
As previously suggested by the actor himself, Fox is currently said to be negotiating with Duchovny to return to the series for far fewer episodes, possible 6-9 for the whole season, in a deal which the trade says will involve "big bucks."
It appears that after the lawsuit, Duchovny was (according to official press release) going to pursue acting in different roles to get out of being typecast as the "guy chasing aliens". Due to this, he made a deal with FBC to have less episodes during season 8. Adding this all up, it can only lead one to believe the story line was derived from aftermath of the lawsuit and not originally supposed to occur that way.