Work through the usual suspects. (1) Current too low — bump Vref/run-amps up a little. (2) Speed/accel too high — lower max_rate and acceleration; a skipping motor that runs fine slowly is almost always asking too much too fast. (3) Mechanical binding — disconnect the belt and spin by hand; stiff spots, a misaligned rail or an over-tight wheel cause stalls. (4) Wrong steps/mm or microstep mismatch between firmware and driver jumpers. (5) Noise/brown-out from sharing the wire supply — separate them.
Isolate by testing one axis, slowly, unloaded. If a TMC2209 overheats it will pulse off — add cooling. Most 'random skips' are heat-versus-feed on the wire fooling you, or accel set too aggressively.
Isolate by testing one axis, slowly, unloaded. If a TMC2209 overheats it will pulse off — add cooling. Most 'random skips' are heat-versus-feed on the wire fooling you, or accel set too aggressively.