Some of my guinea pig are avid digger/burrowers. The only thing that I have found that really stops them burrowing under their fleece bedding long term is to give them what they want.
What I mean by this is give them fleece to burrow under in a way that you are happy with. I have several small blankets of fleece (most are about 20 to 30 inches in size in both width and diameter, all of them prepped so they wick moisture), and when I clean there cage I toss one of the small fleece blankets (I call them the decoy fleece) in on top in a corner for them to burrow and lay under. Two of mine will cart them all over the cage, the other two keep them in just the one favourite spot, but it keeps them happy and keeps the full cage lining fleece in place. These decoy fleeces do get changed out regularly in my cages simply because of how popular (thus heavily used) they are.