would be interesting if they have something implemented that does this indeed.
But what i do always is to create a new efi partition aside from the windows one if i create dualboots.
Issues can be different things also… as i see the case that the boot entry in the “Bios” is removed this is an entry written into the motherboards nvram not on the boot partition.
In this case you can simply recreate the entry from booting and chrooting on a live ISO bootctl install --efi-boot-option-description="YourFancyName"
The second case is that a windows update is recreating the efi partition and with this removing kernel images and boot files completely… recreating will work too, you can use this as a guide: [Tutorial] Convert to systemd-boot
Basically you need to reinstall bootloader (systemd-boot) and recreate the kernel images plus generating the needed systemd-boot entries