We were on our third coat of water based polyurethane on my hardwood floor and ran out. I went and grabbed a can and when I started putting it on I noticed a difference. It was oil based. The area now looks completely different. It's like a 4 by 6 foot area. Should I try to sand it off? We've come so far, I would have to hire a professional at this point. Any advice would be greatly appreciated!
You have a few options:
Don't put any more Brand B on. Go get more Brand A and finish the rest of the floor. After it has all cured, place a 5' x 7' area rug over the Brand B area.
Continue with Brand B over the rest of the floor. Yes, it will look different than you originally expected, but at least it will seem like it is supposed to be that way. Who knows? In time you may prefer the accidental finish.
Rent a floor sander and either strip off the Brand B area, or the whole floor. With the former, you could get lucky and be able to re-polyurethane the one section to match. If so, stop. But odds are you'll never get it to look seamless. So either use one of the methods above, or strip the whole floor.
how large is the room that the bad section is in? if its small, just redo the whole room. even if you hire it out, its only going to cost you $3-$5/sq ft. if you want to do just the section, with no dust, but spend way more time, try this.
1) strip the finish down to the bare wood with acetone and lots of paper towel. wear a VOC rated respirator. work small sections and be liberal with the acetone and the scrubbing. have a fire extinguisher handy and only use a spray bottle to apply the acetone (that way if you have a fire, it will be small compared to pouring buckets of the stuff on). you can use a stiff bristle brush in the direction of the grain. it will be slow, but it does work on all latex and most alkyd polyurethanes. if it wont come off, you may have to use MEK or methylene chloride, but these are bad chemicals and need special handling precautions. strip the area of the wrong material right back to on top of the correct topcoat. do not tape anything yet to mask an area off (the acetone can migrate under the tape and strip the tape line, or worse, fuse the tape adhesive to the topcoat. 2) tape off the area. restain the exposed areas. usually the pores in the wood that are still closed off with urethane are lightened by the acetone, and the new pores that open up from the acetones use absorb less stain than sanded pores do, so the whole thing just kind of balances out. if its new stain, just match its general depth of colour as best you can. if its old stain, go lighter as stains tend to darken over time. if there is no stain on the floor of any kind, just continue. 3) topcoat with the correct top coating
NB - matching wood colours and stains is an art that takes years to master. wood species vary wildly in how they react to this process and results are up to you. test spotting areas is a great idea. once you have a protocol that works, just start again and redo the whole area to match the test area that worked.
Based on your description, the oil based poly is not compatible with the water based you started with. The only sensible way to fix it would be to remove the oil based poly without disturbing the stain below it.
I read that an equal mix of lacquer thinner and denatured alcohol will do the trick to remove the poly without damaging the stain. The recommendation was to mix the two and apply it to the area with a paintbrush. Let it soak for a few seconds and scrub the area with fine steel wool. Then wipe the area clean with a cloth, and then wash it all off with a mild wood cleaner and let it dry.
After doing that, lightly sand the area with fine sandpaper, being careful not to sand into the stain. This step is necessary to smooth out any bumps of old poly left over. Since you already had applied a couple of coats of water based poly, there should be a layer of water based poly that will protect the floor while you do this.
After the oil based poly has been removed, then you can go ahead and reapply the water based poly. You may need to do additional sanding to feather in the finish to the rest of the floor. After a few new coats of poly, it should blend in with the rest of the floor. Try to have a slight overlap between the good area and the area you are refinishing. If the finish still doesn't match exactly, you could apply one last coat of poly over the entire floor.
Wait for the oil-based sealer to harden and than using an orbital sander with 150 grit paper sand the area of oil-based sealer. Sand until the sealer becomes opaque than change grit to 220 and sand until the area is level with the water-based sealed floor. I believe if you look at the directions on the can it will state to sand between coats if more that 24 hours has elapsed, so sanding a sealed floor won't harm it. Vacuum any dust wipe with a damp towel, let dry and continue sealing as before (using the water-based sealer). Don't try to dissolve the sealer with solvents. You are just going to make a huge mess.