Upload whole system manual?

Our policy is to submit the whole Cx Report and Systems Manual, but while we have had large files, nothing as large at you mention. Large parts of a Systems Manual can be manufacturers information or repetative. You might try including some information for each heading in the manual, then indicate that some content has been deleted to conserve size. At most, they might ask a question, but I would not expect an immediate rejection. On projects where we have been commissioned, we have seen much less submitted and accepted, but don't feel that is good practice.