newort2001,
Air in the returns could be entering anywhere on the suction side of the pump. This includes underground piping and the skimmer. Pull the float assembly(if there is one) and basket out of the skimmer, check the weir gate to make sure it is moving freely. Run the pump and see if the air continues. If there is a valve at the equipment splitting the skimmer and main drain, then try closing off the skimmer and main drain separately to see if the condition changes.
Shutting off the equipment and allowing the pool water level to drop is the next thing to do. The water will stop at the level of the leak. If it's a leak in a pipe at the bottom of the skimmer the water level will drop to that level as an example. If it's the suction line going to the bottom of the pool(main drain line) the water will drop below all fixtures/pipes that enter the pool.
Do the same with the spa suction/returns.
Common areas that leak that are non plumbing are: skimmer throat where peb-tec meets plastic skimmer, around light niche, light niche conduit, around any plastic pipe entering pool including return lines and suction lines under grates, And anywhere underwater where peb-tec meets other materials such as rock, etc.
Good luck.

Answer to your main question:
Having the pebble exposed for a while should not hurt anything.
I have seen pebble pools empty for years, and the pebble has been fine.