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I think you'd be fine to add water, even though the liner hasn't pulled in to the bottom.
HOWEVER, let me ask you a few questions before you proceed.
1) What is the floor made of (sand, vermiculite or crete)?
2) How far down the wall is the end of the vac hose (and what kind of vac are you using and what size is the pool and where is the vac)?
3) Did you duct tape all the panel seams? (also, are the valves closed on all the system equipment, tape off the skimmer lids as well as the light conduit)
4) Did you have a water issue when the pool was installed that required putting a layer of gravel down, to keep the ground water at bay?
What kind of steps do you have?
Sorry for all the questions, as well as some I may have forgotten(on the plus side, this may help me finally write a stickyable 'how to drop a line post'
)
Please let me know how it's going.
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