I hope mod community is not totally dead..
It's not dead. It's just resting.
No, seriously, the mod community isn't dead, but it's not seeing much activity lately. Same can be said for the forums in general.
As for your problem, the only way to make this work is, to add an upgrade-target tag to your new versions, and change it to refer to the original improvement. Like this:
<Improvement>
<S_InternalName>InitialColony2</S_InternalName>
<S_Name>Advanced Colony</S_Name>
<PlacementLimit>1</PlacementLimit>
<AI>0</AI>
<S_UpgradeTarget>InitialColony</S_UpgradeTarget> <S_Type>Normal</S_Type>
<Maintenance>10</Maintenance>
<Cost>0</Cost>
<S_IconName>NeutralCivCapitol.png</S_IconName>
<S_QueryGraphicName>NeutralCivCapitol.png</S_QueryGraphicName>
<CanHaveAgents>0</CanHaveAgents>
<Indestructable>1</Indestructable>
<S_TechRequirement>0</S_TechRequirement>
<Industry>16</Industry>
<Food>10</Food>
<Research>16</Research>
<MoraleBonus>15</MoraleBonus>
<S_InvasionMovie1>NeutralCivCapitol_Normal.bik</S_InvasionMovie1>
<S_InvasionMovie2>NeutralCivCapitol_Smoking.bik</S_InvasionMovie2>
<S_InvasionMovie3>NeutralCivCapitol_Damaged.bik</S_InvasionMovie3>
<S_InvasionMovie4>NeutralCivCapitol_Ruined.bik</S_InvasionMovie4>
</Improvement>
Same goes for the upgrade of the Capital City.
Still, there is one problem with this approach. Unless you make the tech, that unlocks those upgrades, available to all races, there is a possibility to permanently lose the building. This is a problem with the one-per-planet restriction. The game registers an upgrade as a new building. So, if you loose the building, the game doesn't allow you to replace it, because it thinks, that you still have one. The Indestructable-tag should prevent this from happening with your upgrades, but it is something to keep in mind for other improvements, that don't have the tag.
Well, I hope this answers your question.