It's difficult for me to tell for sure because I don't use such shoes but from what I have observed when some of my organ students play is that it gets easier with time.
One student recently came to the lesson with a new pair of shoes. I asked her how she felt (she was playing chorale prelude "Wir glauben all an einen Gott" by J.L.Krebs with double pedals). She performed it with some pedal mistakes, more than usual, actually.
The next week her pedal playing was better and the week after that - almost without mistakes. So I think it takes about 3 weeks of daily practice to adjust to new heels and new shoes in general. She confirmed this idea.
There are some women organists who play organ with extremely high heels flawlessly. How do they achieve such perfection even playing pieces which have passages of pedal scales and arpeggios?
The answer might have some variables but generally, pedal preparation always helps to make the pedal technique automatic and mistake-free. It takes about 80 repetitions of the same passage to make it second nature over the number of days.