I had a think about these 'refuges'. Presumably, in addition to being secure and friendly, the locations also had to be such that Holmes could enter and leave as Holmes and emerge or leave in a disguise without attracting adverse attention. Also, if Holmes suspected he was being followed, they would need a variety of entrances and exits.

Large public buildings - hospitals, post offices, hotels etc - seem to be the most likely options. (Neighbourly Scotch Fir)