I suppose that sometimes "бумаги" can really mean "documents", but the word isn't used too often in this context especially in formal speech like in newspapers, jourmals, etc. Saying "Ваши бумаги в порядке", a person really wants to convey the idea that everything is alright with the documents or with the papers he has checked or looked through. I remember driving along an avenue with my friend (he was the driver) and we were stopped by a policeman who asked us to produce the driving licence and car insurance. After we had done that he examined everything very carefully and concluded that "Ваши бумаги в порядке". Some of those "бумаги" were really documents (driving licence, car insurance, etc.), but some were papers. so that's an example where "бумаги" has been used collectively in real life.