LOL Krish
Most Bona water borne finishes can go over oil, xylene and alcohol based finishes, but once you go that route your stuck with it. Unless you completely resurface the flooring.
I do not like the idea of applying a different product over another. I'm not a big fan of water borne finishes but they are as green as your going to get. Be ready for a price jump also. Water borne finishes can get very pricey.
If you want to stick to the original finish, just shut the skimmer down and crate a draw of fresh air across the room by opening a window on one side and having a fan pull on the other. Or however you can do it.
Even the water bore finishes (latex) can pollute the air. So I recommend shutting down the skimmer either way.
If your flooring tech is competent though I would trust his opinion since he has been onsite.
Basically it is oxygen exchange your wanting to limit during this time. You could get an air pump with a long line ran outside and set that up to the skimmer so your pulling fresh air in from the out side.
When I exterminate the home I seal off the entire aquarium in plastic and pump fresh air in this way. I shut the skimmer off, turn off the power heads or closed loop, (whatever is causing circulation and oxygen exchange) and pump in fresh air from the outside using a diffuser stone in the display. Always worked for me.
As for water borne finishes, Traffic by Bona is one of the best I have used. I am currently trying a new product from Germany called WS EasyFinish by LOBA that is very nice! I used it on my new stand build also with great results.
