Cannot replicate neither.
I have created a flight plan and saved it to my pc.
Then clicking on “load pln file”, the window shows up with the list of options and I can repeat those steps without any issue.
The options “LOAD PLN FILE” and “SAVE AS PLN FILE” only work ONCE after a fresh start of the sim and won’t have any effect when invoked again thereafter i.e. the pop-up “Load / Save Flight Plan Files” will no longer appear.
I don’t know what you have tried but I think either a re-install of FS2024 or re-install of Windows 11 must have fixed it for me.
Re-install of FS2024 is easy and quick.
Save Community folder.
Uninstall via Settings, apps, Installed apps, FS2024 & Uninstall.
Install via MS Store.
If you have only FS2024 on another drive, format the drive before you install it again.
In-place re-install of Windows 11 via Settings, System, Recovery, & Fix problems using Windows update.
Clean re-install of Windows 11 and takes around 40 minutes.
Saves your personal data and files.
I think the problem is local to your PC and not something that Asobo/MS can or will fix for you.