The spots probably came from a bacterial/fungal issue, maybe some cold. The spots haven't spread, so I wouldn't worry about them. They sank a bit as the damaged tissue dried. The damaged areas on the leaves will just be there until the leaf drops in the normal course of aging (which could be a year or two) But the leaf is doing it's photosynthesis job so you would not want to remove it - you want the plant to have as much strength as possible, that 's what you need to get flowers... and that's the goal. Orchids develop ugly leaves in the course of living... the flowers make us forget or ignore those imperfections.