I have a flow I was working on yesterday disappear on me today. When I search for its label, it isn't in the flows.json file, but if I go under "configuration" I see components within the "On all flows" I was working on that also includes the nodes.
Can you send me your flow file via direct message?
There is a very rare issue that can cause this that we've never been able to track down. If you can share your flow file with me, I will be able to repair it for you.
If you click on my user icon, you should see a 'message' button (although as I see you've only just joined the forum, you might be restricted in what you can do...). I'll send you a message you will be able to reply to.