Furnace/water heater Flue liner

Currently, I have an older gas furnace and gas hot water heater that share a common flue vent. The vent is a 6" diameter pipe and runs from basement to roof. I am considering installing a 95% efficient furnace. I've been told that if I switch to direct vent on the furnace and 'orphan' the hot water heater vent that the current flue will be too big and I'll have condensation problems in the winter.
It sounds like I can either install a stainless steel liner which won't be effected by condensation, or install a smaller flue pipe which will change the velocity/pressure of the gas and it will be OK.
Can I do either of these myself? What about the flexible aluminum vents, can I just pull one of these through the existing pipe?
By the way, I'm having the furnace installed by pros. They said I probably don't need one, though another company/quote said I did. Just wondering if I have trouble down the road how easy it will be to fix.

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