Yes you can delete them from Lightroom, and doing that will not affect any images that are in the Photos app, but before doing that you should obviously verify that they do still exist in the Photos app.
Do you have a paid subscription? If so an alternative would be to leave them in Lightroom but only store Smart Previews of your images in Lightroom on the iPhone (the original stays in the cloud, but only a smart preview is held on the local device). I have Smart Previews stored locally on my iPhone for all of my 22k images, which takes up about 36gb.
And have you considered deleting them from the Photos app instead, which is what I tend to do. I don't see the point in having originals stored in two separate image editors.