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I just had my gas tank changed and it has an aftermarket petcock without a fitting for the other end of the VOES vacuum line, it’s been plugged and runs fine, does anyone know if that will affect the VOES itself.
As long as the now-unused line is plugged off, you're fine.
^^^This^^^
That said I'd replace the vacuum line with a singe hose going straight from the intake to the VOES.
Doing so will eliminate several possible points of failure (the T junction and the plug for the petcock) not to mention giving you a nice new line instead of the however many year old hose that is on there now.
Originally your bike had a T-piece in the VOES hose, with links from the inlet manifold to the gas-tap and the VOES itself. Your 'new' tap removes a renowned unreliable thing, so as suggested above, simply use a single length of hose from manifold to VOES and dispense with the T-piece.
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