I have 40k prestige,
2nd city is a ‘loose end’
Ill evacuate the resouces,
how much prestige will i lose if any?
You wont lose any Prestige 
You will Get more Prestige by building in your Only city,Meaning that
1 City (low Townhall lvl) = More prestige
2 City (same Townhall lvl) = half Prestige
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You wont lose any Prestige
You will Get more Prestige by building in your Only city,Meaning that
1 City (low Townhall lvl) = More prestige
2 City (same Townhall lvl) = half Prestige
References :
Experience of 1 Year