You're not going to ruin your liner (unless you use waaaaay to much chlrorine, like in the 20ppm++ range).
We converted to chlorine from Baquacil in 2004. I had just found this message board at that time. There really is no perfect science when converting to chlorine. It was way easier than I thought it would be. I thought we might end up with a yellowish/green mess for an entire summer. I was pleasantly surprised that the entire conversion only took about 3 days, and it was very easy.
Friday night: We dumped in about 6 or 7 large cups (like the old laundry scoops you used to get with big boxes of laundry detergent) - of Cal Hypo shock. Immediately, the pool turned a weird looking yellowish color. Then we put about 5 tablets of Trichlor pucks in the skimmer basket and we put 5 pounds of CYA (stabilizer) in a ladies nylon hose and tied it to the inground ladder. Stabilizer dissolves very slowly, over the course of several days.
Saturday: Dumped another several scoops of cal hypo shock in the pool during the afternoon. Backwashed the filter once in the morning and again later in the evening. The water was already starting to turn more of a light greenish color - I'd call it a "clear green". Saturday afternoon we dumped the sand in the filter and replaced it with new sand, which took a couple hours.
Sunday: Surprise! The water was virtually clear! I couldn't believe it cleared up so fast. I backwashed the filter again, and added a couple more scoops of Cal Hypo shock.
So for us....in about 48 hours, our water was nearly perfect. I realize that for other folks it has taken several days longer...so I'm not sure why ours went so easy.
That was back in July 2004.....so here is an update:
Spring 2005: Opened the pool to a yucky brown color. We had installed a sewer line and a sidewalk near the pool, and evidently all the dust and dirt in the air settled on our mesh cover...and filtered down into our pool water. Yuck. But, it only took about 5 days, a few pounds of shock, and quite a few gallons of bleach, and a quart of polyquat algaecide to completely clear up. The rest of the year was very easy - we always had 100% clear water, no algae or other problems.
Spring 2006: This year, our water was completely clear when we opened the pool last weekend. No construction during the fall or spring months, so therefore there was no dirt or dust in the air to get into the pool.
Overall....chlorine is ten times better than our experience with Baquagunk. And it's cheap too! I spend ~maybe~ $150 in chemicals for an entire year. That includes a couple quarts of polyquat algaecide, about 30-40 jugs of 6% bleach, and a bucket of trichlor pucks.
Good luck with your conversion...and don't be scared! It's not as bad as you think.
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