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I have a question if two rules stack with each other.

The first rule is the Greater Thurian League Custom that reads:
Models with this custom (excluding COG models) count as 2 models when determining control of an objective marker, or 5 models if they have a wounds characteristic of 10 or more.

The second is the Guild Affiliate warlord trait:
In your command phase you can select one friendly <League> core unit within 6" of this warlord. Until the start of your next command phase, that unit has the objective secured ability. If a model in that unit already has this ability, that model counts as one additional model when determining control of an objective marker.

If I have a unit of Hearthkyn Warriors, who have objective secured, and are Greater Thurian League and I use this Warlord trait on them do they now count as three models each when determining control of an objective marker?

Looks like yes.

Absolutely. That is how those two rules would interact.