[squeek.]

Class limits can be changed anytime using those functions. The "must be in startup" thing is just for setting up the initial class limits.

To set a server cvar, you can use SetConvar( convar, value )

EDIT: Changing class limits won't immediately enforce those limits (it'll just make it so players wouldn't be able to choose/switch to that class afterwards). To enforce the limit immediately, you'd have to manually switch players playing the now-forbidden class(es) using ApplyToPlayer( player, { AT.kChangeClassSolder, AT.kRespawnPlayers } ) or something like that.

This sort of thing is done in ff_ksour to disable scouts on Defense.

EDIT#2: The ksour code:
in player_spawn:

	-- wtf, scout or med on d? are you mental?
	if (player:GetClass() == Player.kScout or player:GetClass() == Player.kMedic) and (player:GetTeamId() == defenders) then
		local classt = "Scout"
		if player:GetClass() == Player.kMedic then classt = "Medic" end
		local id = player:GetId()
		AddSchedule("force_changemessage"..id, 2, schedulechangemessage, player, "No "..classt.."s on defense. Autoswitching to Soldier." )
		AddSchedule("force_change"..id, 2.5, forcechange, player)
	end

The scheduled forcechange function:

-- force a scout/med to switch to soli if they haven't
function forcechange( player )
	if (player:GetClass() == Player.kScout or player:GetClass() == Player.kMedic) and (player:GetTeamId() == defenders) then
		ApplyToPlayer( player, { AT.kChangeClassSoldier, AT.kRespawnPlayers } )
	end
end