Sometimes, the older a pokémon gets, the more past injuries come back to haunt them, so to speak, especially if those injuries were particularly traumatic.
However, keep in mind that just because a pokémon can no longer function in certain ways due to physical disabilities doesn’t mean they can’t function at all. You therefore have two options, anonymous. The first is work with your local pokémon center to develop a training regimen that builds your pidgeot’s endurance. There is always a chance that he can regain use of his wing with regular therapy and exercise.
On the other hand, your second option is to change your training regimen. Focus on quick, powerful attacks (not literally Quick Attack, although this too) and teach your pidgeot either Roost or Toxic or both. When training and battling, teach him to fire off one of his wing- or wind-based moves, then land and use Roost or run about on the ground, perhaps while outlasting an opponent thanks to Toxic.
If you don’t typically battle, train your pidgeot to be quick on his feet (literally this time) and perhaps to use his wings for other means (such as secondary hands, which many handless pokémon can do—take scyther, for instance).
The point of the second option is simple: if your pidgeot can’t regain his flight endurance, then it’s important to teach him other ways of moving or making use of his body so that he can continue to feel valid as an individual and useful at that. The more you can reassure him that he’s valuable to you and your team (or that he is, in general, still a perfectly valid pidgeot) despite his inability to fly as far as pidgeot with perfectly healthy wings, the easier it will be for him to understand that flying and his identity are not inseparable concepts.
Of course, if by “bother” you mean that your pidgeot is in physical constant pain, I urge you to take the first option before trying the second as that would be humane, but aside from that, if your pidgeot simply can’t fly for long distances before his wing gives out, at the very least, the second option may help ease his mind a bit.
Best of luck, anonymous!