Yes, prolonged contact with niter can cause a niter off-flavor.

If there is already sediment on the bottom, gently pour off the clear syrup on the top into a clean jar and leave the syrup/sediment at the bottom. Leave that out on the counter to warm a little (or warm gently in a pan) and then let the sediment (niter) settle out for a week or two, then pour off the clear syrup on top.

Alternatively, as long as the syrup is ONLY for personal use, you could try the very old method of clarifying with egg-whites.
https://wilderstead.com/grow-your-ow...gg-whites.html

Do NOT do this if the syrup will be sold -- eggs are an allergen.