No suggestions, but I do thank you for your post, as I am also in that situation.

What I am probably going to do, barring more experienced suggestions is drain until 4 - 6 inches remain then add 1/2 gal bleach + 1/2 gal algaecide then thoroughly scrub the entire pool, inside and out. The instructions that came with the liner say that it needs to be well dried before folding for storage, so that is also in the plan.