Flooring – Help with vinyl planks on damaged subfloor

Use a heat gun to heat up the tiles and soften the adhesive underneath and pry it up with something (putty knife/scraper/pry bar).

You should be able to buy floor adhesive remover to get the stuff off of the bottom tiles you want to keep. I found some that was a sort of gel that you spread around on the floor and let it sit for 15 - 30 minutes. Then, scrape it up and it would pull some of the adhesive up too. It was not perfect for me (vinyl tiles glued to hardwood) but it worked OK.

The stuff I used is made by Klean Strip and was available at the local Lowes, http://www.wmbarr.com/product.aspx?catid=72&prodid=115

What kind of flooring are you putting down? If it's tile, I'd probably reinforce the floor a bit first with a new layer of t&g subfloor before putting the tile down... which solves your problem.

If there's any musty smell, you can clean the floor with trisodium phosphate (the real stuff, not "substitute") ... but don't soak it. Just scrub it with the tsp and a scrub brush. The TSP will probably take up the glue as well... but has a significant chance of eating your plywood in the process. ;)