On my test PC I have 4 drives with several partitions and lots of different OS systems and versions.
Regarding Linux I have 1 boot partition that is connected to one Linux installation, while the other Linux installations have their boot directory included in the root partition as only the extra partition is used for booting via grub. As a side note I’m only using ext4 for Linux.
Recently I noticed that my boot partition was missing from my partition table and I think I noticed it after I was upgrading one of my Windows Insider installations to build 14393. Fortunately I could simply recreate the partition that appeared as free space with gparted and everything was still there.
Strange thing is that when I updated my two regular Windows 10 installations on that machine (32 and 64 bit) to the latest release, nothing happened to this boot partition. Also none of the other partitions was affected, regardless whether it is used for FreeDOS, Windows (98, 2000, 2XP, 27, 28.1 or 210), Linux (6 installations), BSD, OS X, VMWare ESXi or my two data partitions.