How about this? (Not sure I understand your original dialogue exactly, but I think this is what you want.)
- Have you completed the valuation of documents to be stored in the archive?
- Yes, I have prepared the appraisal report.
- Is everything all right?
- Not yet. ( or Not everything.) I’ve found some documents which must be kept separately.
- Will you bring everything into order? or (bring all documents into order?)
- Sure. Optimal conditions are available for storing documents of this type. (these types??)
- Would you mind if we check/inspect you next week?
- No problem