Since I couldn't find this solution anywhere on the internet, I want to share my solution, hoping it could be useful for someone else.

Context

I have a dual boot with Ubuntu + Windows 11 on my laptop, the first installation was done two years ago on two separate 512GB SSDs with two separate EFI partitions, then on Ubuntu I added the Windows entry to GRUB with os-prober.
Everything worked fine until I replaced the two SSDs with a single 1TB one holding both OSes, I copied the EFI partition with GRUB and all the other ones except the Windows EFI partition.
After cloning, both Ubuntu and Windows booted successfully until the next upgrades on Ubuntu ran os-prober and Windows Boot Manager disappeared from GRUB.

The solution

After an entire day of useless searches this is the combination that worked for me:

1. Boot Windows Installation media or Hiren's Boot CD
2. Open a terminal and use diskpart to assign letters to the Windows partition and the EFI partition, from now on the first one will be C: and the second one will be D:
3. Run bcdboot C:\Windows /s D: /f UEFI
4. Exit and reboot, GRUB is still bootable because this procedure didn't overwrite GRUB files
5. On Ubuntu run Gparted, select the EFI partition and make sure flags boot, esp, no_automount are enabled (this was the actual solution and the most difficult part because nobody pointed this out in any guide I could find)
6. Run sudo update-grub to finally get Windows Boot Manager back

It may be necessary to delete all contents inside D: before step 3, not totally sure, but if the procedure above doesn't work you may have to try this way.
BE CAREFUL: you will completely delete GRUB and you will need to boot a live CD, chroot in your Ubuntu partition and restore GRUB:

#replace /dev/nvme0n1p5 and /dev/nvme0n1p4 with the appropriate devices sudo mount /dev/nvme0n1p5 /mnt sudo mount /dev/nvme0n1p4 /mnt/boot/efi for i in /dev /dev/pts /proc /sys /run; do sudo mount -B $i /mnt$i; done sudo chroot /mnt grub-install --target=x86_64-efi --efi-directory=/boot/efi --bootloader-id=ubuntu --removable update-grub 

Refs:
https://forum.level1techs.com/t/reinstall-grub/134056
https://web.archive.org/web/20250818050000/https://forum.level1techs.com/t/reinstall-grub/134056

NOTE: the sequence provided above is an extract of everything I tried today, it should be enough to make the dual boot work again as all the other trials were useless, even rebuilding the BCD may be useless, since it always has been there. The key part was actually setting the flags of the partition.

I will appreciate feedbacks if anybody tries this fix or finds an easier solution.