I don’t know how it could just happen on it’s own, but sounds like they are either plugged into the wrong connector on the main-board or flip-flopped or something. The X-endstop and Y-endstop should be in the MAX endstop connection points, as they only stop it in the +X and +Y direction respectively (nothing stops it in -X or -Y). Unlike the Z, which should be in MIN, as it works in the -Z direction for stopping (and nothing stops it in +Z).
When you are testing in jog mode, are you running it in +X and +Y directions (toward the back-right corner)? You can also try manually pressing the endstop switch for the opposite axis and see if they are perhaps swapped.
Otherwise, get out an ohm-meter and check each wire end-to-end on both cables. The Y-endstop is stationary so isn’t likely to fail over time, but the FFCP eats X-endstop cables due to all of the flexing during use. Mine died with only 40-50 print hours. But I don’t understand the Y-endstop going out unless it is just a coincidental bad cable… Use the ohm-meter – it’s the only way to know for sure…