Probably obvious but do they show without any conditional? Or seting "1=1" as conditional? Make sure that in the Menu Settings, Document Properties, Security, "Show all Sheets and Objects" is unchecked. Go back to any preivous version and use the same script to see if that works.
When you access to a document that reduces data, that is exactly what it happens: data that is not realted to that user is reduced (read "removed") from the document. Say this way: you have a user ADMIN that has all privileges in your document, and one user SALES that has only access to data and sheets related to SALES.
You first log onto the document as SALES, data is reduced so there's only SALES information left, no PURCHASES, no ACCOUNTS, etc...
Now you close your document and you open it as ADMIN. Yes, ADMIN has access to the whole document but, since SALES already logged in and data was reduced, ADMIN has access to all data and sheets, which are no more than SALES. The rest of the data isn't there, simply.
Hope I made this clear and not more confusing.
There is no other way to get all data back again than reloading.
If you are developing and testing, I'd recommend you to not to check Strict Exclusion even not to check "Reduce data" in the document properties, rather than "Initial selection based on section access".