Could a chipped tiling flange on acrylic tub cause problems in the future

It sounds like one of your valves is not working correctly. It could be that the handle is slipping or that the valve is clogged. Does it feel like the handle is turning the valve, or is it slipping? If its slipping you can probably just tighten the screw.

As far as replacing it, you might get lucky and find a replacement valve, but in the event you don't, they make remodel plates which allow you to relatively easily replace a 3 handle setup with a 1 handle faucet. The remodel plate covers up the area in the wall/tile you'd need to remove to swap it out; you don't have to tear out the entire wall. If you can get in behind the shower you can probably do it without the remodel plate.

Let's look at the three pictures above.

#1 - This is probably the most common install. You cement board is on the same plane as the flange. It is thicker so it ends up hanging over.

Tip - If you are using cement board by itself I would strongly suggest using 1/2 inch. Also I am a strong supporter of hardibacker since it doesn't allow water through or hold water. Durarock is a great product but I use hardibacker in wet areas.

#2 - Some people are going to look at this and say never do it. Well it is done. Two main reasons. First is the tub tub deck isn't exactly flat. Some bow towards the middle. This allows the backer board to almost sit it on some spots and maybe be 1/4-1/2 inch up in others. The second is smaller tiles. If you are going small glass mosaic all the way up not only should you do this but it is a must. If you stagger the backer the bottom tiles could move if hit near their bottoms (especially if you are caulking the deck to tile transition).

Tip - In a lot of my tub surround installs I start with 1/4" drywall, plastic sheet (moisture barrier) then 1/4 hardiboard. This is a fast install, allows you to get something like picture #2 minus the furring strips (which are not fast), the 1/4 inch backer is much easier to get screws in right, and with a total of a half inch you can meet the rest of the room. I read about this install over at the johnbridge forums probably 8-9 years ago and have done at least 20 this way without one issue (2 in my home).

#3 - Same deal as the first picture but with a goofy flange. Again you could use furring strip or drywall.

Tip - Once you fur out the back or the front of your tub you have a dilemma. How do I meet up with the rest of the room. Let's first of all say you need to fur out a 1/2 inch. Wow if you fur out and put up 1/2 inch backer you are out an inch. So that is why I say to keep the drywall+backer method in your back pocket. You can go 1/2 inch drywall then 1/4 inch backer. Also how do you meet up with the rest of the room? Well if it is a small bathroom I have double layered drywall along a wall. This is very easy to do and maybe $20 in materials vs furring out the whole wall - which is harder to match things up. An alternative in this case is to use 5/8 for the rest of your room and transition under tile work. Very easy to build up 1/8 inch using extra thinset.

Normal Install Instructions

1. If you need to push out the install add furring strips or drywall.
2. Staple moisture barrier (plastic sheathing) to the studs (or furring strips or drywall). The plastic should go a few inches into tub deck and above your highest backer board. It if fine to take it to the ceiling too.
3. Screw in backer board using roofing nails and approved screws. First every piece should have 6-8 screws. They are a pain to get flush so use roofing nails for the rest (need at least 1 1/4 inch).
4. Put up your alkali resistant mesh tape on all backer to backer seams (gray mesh sold near backer boards at the big box). If it doesn't say alkali resistant it isn't so don't buy the drywall mesh.
5. I strongly suggest that you hide backer to drywall transitions under tile. When I do a normal tub surround I buy 4 pieces of backer. One goes up vertical on each side (5 feet), one horizontal on the back, and another cut at 2 feet horizontal so that we have 5 feet above tub deck all the way around. Drywall above that . I even do the drywall if tiling to the ceiling. Then the tile is going to at least 5 1/2 feet above the deck and 3 1/2 feet from the wall. No transitions for me.
6. First step of tiling day is to mix thinset a little on the soft side. Go over the joints that have your mesh tape and fill them in.
7. Plan your tiling pattern. If you have to make cuts, hide them in the corner. Plan to never cut your tiles height-wise - just tile a little higher (or lower).
8. Start at the bottom. With bigger tiles you may need to start at the second row and have them sit on a strip until the thinset is strong enough to not sag. Make sure your bottom row is 1/8 inch from tub deck. Note that on curved tub deck you might have to be 1/16 of an inch on some parts and much bigger on others.
9. After you are done tiling cut the plastic right at the tile level all the way around. Push plastic under tile gap.
10. With the new cheap plastic tub you pretty much have to caulk the deck to tile transition. For heavier more solid tubs you can grout this area. I like grouting the bottom because you can always go over it with caulk in the future. People will say to never grout because it will crack. As I mention above it depends on the type of tub.
11. Caulk your corners and caulk the top area of tile.