sbv16, the replies above are from TFP pool owners, scientists, and/or experts who are widely respected and have been in the pool industry for decades. What I'm about to add (lengthy - sorry) is strictly my own personal (similar) observations in our FB pool. My apologies in advance for this lengthy reply, but it hits home for me as well. I feel your pain. Since our pool was installed in May '13, we've also noticed a change in our pool surface from the water line and below. In our case, it looks and feels just like calcium. The surface above the waterline is bright blue and showroom smooth. The minute my finger hits the water line and below it feels a bit rougher and looks lighter in color (chalky). Not bad, but like you, our pool is not that old either. I managed our pool for about a year before learning about TFP and proper balancing. I know I allowed my CSI level to reach 1.0 for too long (scale). In my case,
before the discoloration, there was never a time where my CSI was ever too low which would promote etching. That may be something you wish to reflect back upon from the past 3 years. I also can't imagine that an elevated chlorine level would cause any harm, especially when a reasonable level of CYA (stabilizer) is maintained as a buffer agent.
I see your pool store and manufacture disagree.

No surprise there. In regards to your pool store's comment about etching, most FB pools manufactures I have contacted do not use calcium-carbonate in the fabrication process, so you wouldn't think a low CH would be as detrimental to the surface like it would be for a plaster pool (etching). I'm not saying it's impossible, but our pool manufacture stated that it would be very difficult to damage the gelcoat as they apply numerous layers during fabrication. As a side note, it is still good to maintain an adequate CH level to protect the shell from staining (see TFP recommended levels).
Then your manufacture mentioned calcium. Our FB pools certainly can get scale. In my early days of pool ownership, I had a habit of letting my pH get a bit elevated. So an elevated pH, coupled with an elevated TA and local hard water (CH), was a recipe for calcium scale. Once I understood what happens when the "CSI-trio" of pH, TA, and CH becomes elevated, I believed that I may have allowed the situation (calcium scale) to occur. Again, that may be something you wish to reflect back on from the past 3 years if you kept testing records.
Now I keep a spreadsheet with all my daily tests. Since I attribute MY discoloration to scale, I have been trying to reverse that trend by keeping my CSI in the negative to see if there is any change. It's been about 1.5 - 2 years now and I've yet to see any real productive change. Perhaps a little bit better, or maybe it's my eyes playing a trick on me (wishful thinking). To-date, I'm not seeing the change I was hoping for yet. As noted above, perhaps it's simply that any attempt to remove scale via a lower CSI may take longer to remove than it took to get it on there in the first place. Not sure. As for other methods of calcium removal, we can't use wire brushes in our FB pools, and those so-called scale removers from the pool stores are useless. As noted above, we could scrub or sand an area and see a subtle improvement, but I can't do the whole pool that way, and I don't want to damage the gelcoat or end-up with an uneven appearance. I haven't tried what you did (acid directly along the water line), but perhaps I should as a test.
In the end ...... sorry, I said this would be lengthy.

But in an investment such as ours, you want the pool to look showroom perfect for years. Any imperfection is frustrating. Since
our pool discoloration is uniform, feels the same way throughout, and
I know my CSI was elevated and
NEVER too low (etching), I'm hoping it's just scale from my early "pre-TFP" days. I'm still optimistic that a few seasons of negative CSI may resolve it. Aside from the lighter color blue underneath, the pool looks great and everyone compliments us on the pool and water. Again, something that may help you is if you have records of tests and/or can confirm where your CSI level (pH, TA, and CH) was the past 3 years. That info may help give you a good path forward. I just figured I'd pass-along my own personal FB pool experience and let you know you're not alone. FB pools are pushed as being very easy to maintain - mostly because of their smooth surface. But they are not excluded from scale or other gelcoat problems if chemical levels are allowed to go unbalanced for a significant length of time. Hopefully we've given you some good information to go on. Best of luck.
