This is a really interesting question!
The navigation system of the drone will have to grapple with being in a rotating frame.
tl;dr: While the drop-off of gravity with altitude would be mild and manageable, the Coriolis force will be huge and absolutely have to be built in to the maneuver planning system of an automated drone.
Rapid drop-off of gravity with "altitude"
Centrifugal "gravity" won't behave exactly like regular gravity.
On earth, the force of gravity points almost exactly "down" wherever you navigate around the spherical Earth, and it falls of with altitude very slowly:
$$g(\text{alt}) = g_0\frac{6378^2}{(h+6378)^2} $$
where $h$ is altitude in kilometers. You'll need to rise by about 32 kilometers in altitude for gravity to drop by 1%.
But centrifugal artificial gravity increases linearly with distance from the center, and it points away from the cylindrical axis rather than towards the center of a sphere. So if the radius of the cylinder is 10 kilometers, then
$$g(\text{alt}) = g_0 \frac{10-\text{h}}{10}$$
where $h$ is altitude in kilometers.
In this case gravity will drop by 1% after only a 100 meter rise!
That means that the drone's navigation software will have to be careful to recalculate it's gravitational mass regularly, and completely separately from its inertial mass and moments of inertia.
Coriolis Force
The other consequence of artificial centrifugal gravity is the Coriolis force. This is a fictitious force or pseudo force that "exists" when you are moving in a rotating frame and try to account for things as if the frame weren't rotating.
To get an artificial gravity equal to Earth's $g_0$ of 9.81 m/s^2 at 10 kilometer radius for example, we can calculate the rotation rate $\omega$:
$$g_0 = \omega^2 r$$
$$\omega = \sqrt{g_0/r}$$
gives $\omega=$ 0.031 radians/sec. The magnitude of the acceleration due to the Coriolis force is then
$$a_C = 2 \omega \ \mathbf{\hat{z}} \times \mathbf{v}$$
where $\mathbf{\hat{z}}$ is the unit vector along the axis of the cylinder. A radial velocity would produce an acceleration in the angular direction (in the rotating frame) and vice versa, with a magnitude of $2 \omega v$.
To be 1% of $g_0$ you'd only have to be moving at about 1.6 meters per second (5.6 km/h) in our 10 kilometer radius cylinder. That's huge!
The drone navigation system would have to plan its maneuvers very carefully to account for the Coriolis force!