It will certainly screw Chile's expansion in Patagonia, to the point it may not happen at all. If the Spanish manage to hold it, they will have the advantage that Chile needs to deal with the Mapuche before becoming strong in the area. Also, the people in Chiloe were pretty independent so they disliked to be controled by someone else. Giving autonomy to them is of extreme importance
A Spanish Chiloe won't have much effect in Argentina, Uruguay or Paraguay, but it will certainly make Chile and Peru to be more militarized.
I think it could lead to two scenarios. One where Chile is unable to settle in Punta Arenas and colonize their side of Patagonia because of the sole presence of this Spanish stronghold, which leads to Patagonia being Argentinean or British. And the other where Chile's expansion is done by crossing the Andes and thus leading to a war with Argentina.
The thing is that it all depends on how well defended the Island is and how much importance is given by Spain. Spain will certainly claim the whole Patagonia, but having a strong presence in the Pacific side is difficult. Chiloe is the only really good land in it. Settlers will be scarse before late 19th Century, and military presence, especially the navy, will have to be in a really good shape, because Chile will try to take the island.