Hi Blunderdog and welcome to GoY. Could you explain why you put sand and soil in to start with? It isn't usual but you may have a reason.

Builders sand in the pond is not a good idea because it contains salt that can kill plants, and certainly won't do any pond plants any good. I use soil sometimes on a pond build, just ordinary topsoil from the garden, but more usually I make 'growbags' from hessian sacks, and plant into them. That contains the soil, and the sacks re easier to position in the pond than the mesh plastic pots sold for plants. Phil

I actually find the large mesh pots work really well for me and after trial and error tend to use gravel rather than soil as it does not discolour the water.

I hope you put sand or a fleece before laying the liner?
I really cannot see how you can get this out unless you drain it and it does need to come out.
I put large baskets in mine with aquatic soil and cover in pea shingle. I find if I rinse the baskets first and drain they dont spoil the pond water. Over the years debri collects in the bottom of ponds so adding some to start with will mean you have to clean it out quicker?