I hide a customfield from all screens through field configuration which my project use. It will be hiding correctly on screen and immediately I modify some fields in my issue and do update. Now the issues which were visible earlier not shown in issue navigator.
Could you tell us what the JQL is for the issue navigator?
It sounds like your JQL is selecting issues based on the fields you have hidden, so it makes sense that they'd be dropped.
As an example, if you have a field "colour", your JQL says "colour = red" and then you hide the "colour" field in project X then JQL will be going "oh, well, issue X-123 doesn't have field colour, so it's not selected" - doesn't matter if you've got data for the field already, you've told Jira the field isn't there for that project.
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