True, in "reply new", you lose the "re: " subject line"" and just get a blank subject field. Obviously, since the intent of replying "as new" is to break the conversation thread and start a "new" thread with a new subject.
As for "reply" and "reply clean", I've played around with those and I fail to see any difference between them at all. I still await "expert" advice on that.
I did come across this comment in a reply from the developers in this forum on March 2 2014:
"On (the) other hand, reply and forward commands in the menu (not the icons) are for special cases, one of them (reply clean) does not add quoting prefixes, and this is deliberate (that's the point of this command)."
That seems like a pretty clear and straightforward explanation, except that the "quoting prefixes" referred to are those little carats > >> >>> scattered all over the place to mark off quoted text. Anyway, most emails I've seen (GMail, Outlook, AquaMail, Fastmail, etc) don't use those carats as "quote prefixes" anymore. They use those long, indented vertical lines on the left side to mark off past message text (kind of like a folder tree). And "reply clean" definitely doesn't remove those lines, though it may have removed those distracting carats in days gone by.
My conclusion, unless I hear otherwise, is that the "reply clean" is pretty much a dinosaur, a white elephant, a useless appendage, which doesn't do anything anymore any different from the ordinary "reply" button, especislly since the "quote prefixes" it was designed to remove don't exist in modern emails anymore.
If it doesn't do anything, maybe it should be retired. Outlook and GMail Android apps don't have such a command.
What might be helpful is a new command to "reply without quoting". The only way to do that now seems to be to change the global settings to not include quotes in any and all replies. And selecting and deleting all the quoted text in particular a reply is a bit of a pain.
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