Apparently, it is working as expected. We need to look at your section access to check why you are losing part of the data, but it may be just the right result of the security rules implemented there.
When you reload, QlikView must present all the data so that when you save, everything will be in the qvw.
After you close and reopen, QV will actually apply the section access and present part of the data.
Check the fields that you are using to control sections access. Try to make the same selections that would happen when the qvw is opened and check the results.
You can also make the selections and use file -> Reduce data -> Keep possible values to understand the results of your s. access.
Hope this helps