.cfg mods during upgrade 🔗 link

I'm looking at the 4.3.17 release (Thank you, Herick) I was able to build and install without an errors (even on Solaris!).

It all worked out, but I noticed a few configuration files needed a little help and I'm looking for guidance regarding best-practice with these.

:: protocols.cfg ::
I have modified a few of the stock protocols. My modifications were moved to the bottom and the stock entries were re-inserted.

For example, I have created column-aliases for a test with:

#  Create an alias to reduce confusion with ldap query tests
[ldap|ldapPort]
   port 389

and after the version upgrade, my file contains:

[ldap]
   port 389
...
[ldap|ldapPort]
   port 389

I just edited the file, removed the re-inserted lines, and replaced my comment line. What is the suggested way to handle this? Even if just leaving the dual entries is acceptable, I've lost my comments so my future-self will be confused.

:: tasks.cfg ::
Almost the same as protocols, but I discovered the tasks.d directory and I've moved my tasks into a file in that location. Should I expect files there to remain un-touched during upgrades?

:: graphs.cfg ::
Just like protocols.cfg. My new lines are present but my comments have been stripped. I can re-insert them, but should I expect to do this step with each upgrade?
I haven't studied source on this yet. Is there a similar "directory" directive for graphs?

:: xymonserver.cfg ::
Arrgh. My comments are gone! Is there some way to flag the comments for retention, or do I need to relocate them to massive README in another directory.

-- 
    Do things because you should, not just because you can.

John Thurston    XXX-XXX-XXXX
user-ce4d79d99bab@xymon.invalid
Enterprise Technology Services
Department of Administration
State of Alaska

Well, based on your experiences, I would suggest backing up the
configuration directory before an upgrade. I put my cfg files in subversion:
this means one can easily see the differences created, and one has the
backups (and history). It's fairly easy to merge different versions of files
with a tool like KDiff3.

Kind regards, 
SebA