I see a potetial problem or two.
A old installation is updated with a image with PR 2698. After that the user does getedid which changes syslinux.cfg, but it is a UEFI system with a existing /flash/EFI/BOOT/syslinux.cfg and getedid only changes /flash/syslinux.cfg. So the UEFI system will still use the /flash/EFI/BOOT/syslinux.cfg which is not changed.
getedid will continue to update /flash/EFI/BOOT/syslinux.cfg if it exists AND the user has booted using UEFI. If the file doesn't exist (never installed, or deleted by the user) or the system is not booting with UEFI, then getedid will update /flash/syslinux.cfg.
Move the /flash/EFI/BOOT/syslinux.cfg to /flash/EFI/BOOT/syslinux.cfg.off will solve that. Deleting it may destroy work in syslinux.cfg what somebody did on his box.
Cleaning up an existing installation is likely to be a case of damned if you do, damned if you don't.
Moving /flash/EFI/BOOT/syslinux.cfg to /flash/syslinux.cfg is all fine, so long as the user doesn't mind having their non-UEFI config overwritten (which may contain custom changes).
And if we were to delete /flash/EFI/BOOT/syslinux.cfg then again we're potentially losing custom changes that may not be in /flash/syslinux.cfg.
Currently (in PR2698) we do neither, *except* when the user is booting in "run" mode when we know the file we're deleting is always an exact copy of /flash/syslinux.cfg, so no custom changes will be lost.
After PR2698, clean installations will not have /flash/EFI/BOOT/syslinux.cfg, but users with upgraded installations can choose to move or delete the file if they wish (and they should, to avoid future confusion).
Going forward I imagine any documentation will refer only to /flash/syslinux.cfg as referencing two files is confusing, and we'll just have to deal somehow with legacy installations (ie. "Delete /flash/EFI/BOOT/syslinux.cfg - you don't need it").