Glad @FurkanKaracan, that you have resolved the issue by restarting the IDE and redeploying it.
Function.json file missing issue will be caused if the function project is deployed with Runtime Issues.
- That file is generated by the Function SDK in
.csproj file Microsoft.NET.Sdk.Functions NuGet Package.
- Any Changes to this file configuration code bindings are not allowed.
I have checked the following test cases to make the function.json file missing in the Code+Test menu:
- Disabled the Function and redeployed from local IDE.
- Published Several times by making function code changes through IDEs and CLI Commands.
- Checked the Kudu Site of my Function App for every publish/deploy.

That file was visible perfectly how many times I redeploy the project to function app in the Azure Portal.
As per my experience, it might be some deployment issues while publishing.
Refer to this MS Doc for more info on function.json file.