1) I would presume it depends on the type of refit. for computer components and such, if it follows reality, the old space in the ship might be slightly reconfigured to accomodate the newer comptuer systems and such. For gross structural upgrades (like the TOS Consitution class to the TMP Constitution Class), then depending on the upgrades nature, then yes.
2) hmm...well, there isa Silent Running option in the online Expanded ship operations manual by KillerWhale. I'd have to look at that before I could give a better answer
A brave little theory, and actually quite coherent for a system of five or seven dimensions -- if only we lived in one.
Academician Prokhor Zakharov, "Now We Are Alone"