First, it better be a Silent Greater Dispel, and even than it takes a good dice roll. Greater Dispel tops out the levels you can add at 20, while the target can carry all the caster levels of the 25th who cast it.
Second, Dispel (Greater or otherwise) can be used as an area effect, or targeted on a person or object.
Since the areas overlap, and the Dispel area only needs to overlap with the areas of the Silence spells, not with the center, it wouldn't be hard to pop them both with the one spell.
Start with the presumption that a 45th level caster has See Invisible and Arcane Sight up permanently. He'll know that there are two Silence spells. He'll know where they're centered, and he'll know where they overlap.
If you center it on an object that you throw, expect him to kick it away or otherwise shed himself of it.
So don't attach it to a stone or coin, attach it to a Tanglefoot Bag so it will stick to him and be a pain to get rid of.
Have your own Counterspells ready for his Greater Dispell(s). He'll only have so many of them, after all, while you can come armed with a Wand, Staff or Scrolls holding as many as you need.
Come with Disintegrates in number, to blast through the Cube of Force he'll almost certainly have. Inside one of those he can blast away with magic while being completely safe from any return fire.
Prepare scrolls with several spells in sequence, designed to take down Prismatic Walls and Spheres. It's a specific series of spells in a specific order. Think of these as magical "breaching charges". You'll need them.
Use Dust of Disappearance liberally. Ordinary See Invisible and Invisibility Purge won't pierce it. He'll need True Seeing, according to the DMG.
Use off the wall stuff, like Dust of Choking and Sneezing. Prepare gaze spells, to keep him busy through his Wall of Force, Force Cage and/or Cube of Force defenses.
Be prepared to keep hitting him, round after round, with such a wide variety of stuff that he can't possibly have prepared defenses against all of it.
Use the "Portable Hole + Bag of Holding" land mine, if you can break his tower's Dimensional Lock effect. Dragging him away from his home field advantage can be a game changer.
Use the Iron Bands of Bilaro item, or whatever it's called. Yeah, it's a one-shot wonder type knockout punch, and is unlikely to work, but you can't win if you don't try.
Presume that he'll have an SR that's through the roof, and prepare a boatload of spells that ignore SR. Fire Seeds is a wonderful one in that capacity.
Be aware that, according to the Epic Level Handbook, Constructs can be possessed and controlled under some circumstances. A Golem body under a Hat of Disguise can make him waste a lot of spells trying to deal with something that's immune to them. It can also pound him to bloody hamburger while he's trying.