Ok, thanks for the feedback.
I myself has 4 $esp's. One for windows, one for all linux OS's, one for my own grub dedicated partition and another for bootctl (systemd boot).
All works fine. But I mainly (now) use my own $esp to boot everything. Left the bootclt in disarray (do not maintain the many kernel changes that needs manual intervention) and install all linux OS to that linux $esp but boot all (including windows) from my grub. So far so good.
I ask my question because I've not messed up windows yet, but from what I've read, if the $esp is shared (usually the case for most people), and windows restored its boot, linux boots get wiped out too. Good to hear this is not the case with you.
Cheers, take care.
ps: I have 2 Bodhi 4's. One in uefi/gpt and another in bios-legacy/msdos. Both working great (Bodhi had always been working great since I used ).
And the one on UEFI, I've changed to yakketty (16.10); I know, at my own risk. Also, I boot up my custom remastered Bodhi isofile more than the installed OS's.