Jaffar is forced on Night of Farewells, and then he can probably come to Cog of Destiny, Sands of Time, and Victory or Death. The other chapters after he joins have pretty limited deployment spots and Jaffar isn't really good enough to warrant taking them. So 4 chapters of being decent late-game.
Jaffar should be beating out Lyn as a combat unit lategame, however, I would think Lyn's great offense early on with Mani Katti, ability to recruit Legault/Heath/Rath/Wallace/Karel/Nino, being required to use to get Geitz, and being forced onto a few chapters more than counteracts this. If Lyn starts building up negative utility or whatever if you use her much past midgame or so, then just drop her from the main team and only use her when forced/when you have enough slots. She already contributed her part, and with negative utility considered I'm not sure Jaffar would even get to go to 4 chapters.
Jaffar should be beating out Lyn as a combat unit lategame, however, I would think Lyn's great offense early on with Mani Katti, ability to recruit Legault/Heath/Rath/Wallace/Karel/Nino, being required to use to get Geitz, and being forced onto a few chapters more than counteracts this. If Lyn starts building up negative utility or whatever if you use her much past midgame or so, then just drop her from the main team and only use her when forced/when you have enough slots. She already contributed her part, and with negative utility considered I'm not sure Jaffar would even get to go to 4 chapters.