I recently started watching the series on Netflix, and I have been watching the episodes in air date order (I am currently about halfway through season 4). I noticed that from season 4 onward, some of the episodes air out of production order, and I'm wondering how often this interferes with the chronological order of the episodes. For example, the following episodes aired out of production order in Season 4:
12. Leonard Betts (4X14)
13. Never Again (4X13)
14. Momento Mori (4X15)
15. Kaddish (4X12)
Having just finished those episodes, it would have made more sense to watch them in production order. "Leonard Betts" ends in a cliffhanger that sets up "Momento Mori", but "Never Again" airs between them and disrupts the continuity. "Leonard Betts"/"Momento Mori" set up an important arc for Scully; "Kaddish" is entirely stand-alone and makes no mention of Scully's arc, so it would have been nice to get it out of the way before said arc was established.
That said, are there any areas in seasons 5-9 where the airing order conflicts with the chronological order? No spoilers, please.