If you want the three-way switch to still function as such, you may find the MS-B102 (pdf) or the OPS or VPS series devices (pdf) useful (as pointed out by ThreePhaseEel in the comments). If you aren't able or willing to replace the motion sensor, though, read on.*
Since the circuit was originally a two-switch light circuit, it's almost certainly wired as a three-way switch. A three-way switch is usually wired with a 3-conductor (plus ground) cable, as in the following image (ground not shown):
(image originally from Wikipedia and modified by me)
As you can see, no matter what state the switches are in, switching on of the two switches will change the state of the light bulb, either making or breaking the circuit.
It's most likely someone replaced one of the original manual switches with your Lutron device, leaving either the red or the black wire hanging loose (hopefully protected with a wire nut, but you never know).
I would like to wire the flip switch box to stay in the on position permanently, remove the switch and install a covered plate to close off that location
This is likely the only option for safely disabling the manual switch. You will need to disconnect the power at the breaker panel, pull the manual switch from its housing, and inspect its switch box. In that box you should find one 3-conductor cable (if North America: red, black, white)** from the other switch, and one two-conductor cable (black, white) going downstream to the light fixture.
First, determine which of the two hot conductors (red or black) was left dangling in the motion sensor switch box. (I'll assume it's the "red" one for the rest of this post.) Cap the other end of that "red" wire inside the manual switch's box. (Both ends of the "red" conductor should now be capped with wire nuts and it's now just an unused piece of copper in the walls.) The other motion sensor hot conductor ("black") will need to be wire-nutted to the black wire from the 2-conductor cable. The two white neutral conductors should already be tied together in the box. Check as well if the box is grounded (bare-copper ground tied to each other and to the box if metal).
In summary: "red" to nothing, "black" to black with a nut, white to white with a second nut.
Once you've safely tied everything together, close the box with a blank cover plate and restore the power to the circuit.
* and if you do want to replace your motion sensor, note that the wiring will be completely different from what is described here. Follow the instructions that come with the new sensor instead.
** if not in North America, the neutral conductor is likely blue, and the two hots will be brown and black. The grounding wire may be bare copper, green, or green/yellow striped.