Unless the underlying infection can be controlled, there is a strong likelihood of return of the cyst or development of a similar cyst in another location on the feet. Allergies and immune mediated disease can be the initiating causes of interdigital pyoderma. Often, if this is the case, there will be other skin disease or chronic ear infections in conjunction with the foot problems. If Demodectic mange mites are present they can cause severe secondary bacterial foot infections as well. Since most clients recognize the term cyst and few recognize the term granuloma, vets tend to mislabel these as cysts for convenience sake.
Some cancers can resemble cysts when they occur on the feet, as well.
The most notable of these are probably melanomas which seem to occur on toes pretty frequently. It is hard to prevent recurrence of these without amputation of the toe or even the leg. These are clearly not cysts when examined after removal. These are benign cysts and complete removal should eliminate them. Dogs that are prone to cyst formation, especially epidermoid cysts, tend to get more than one of them, though.