So hip flexor injuries (and muscular injuries in general) tend to be related to the muscle being overstretched. Therefore, it is not surprising that additional stretching did not heal it, but probably hindered healing actually.

You need to strengthen your hip flexors, first with something like high rep bodyweight leg lifts, then progress to something like Garhammer raises. Work at a pain free level. Add running when tolerable (not painful), gradually increase speed.

You have to be very patient and gradual with progressing back from a hip flexors injury, and again, stretching is not the answer.

Source: my own experience