With Waterfox 53.0.3_2 on FreeBSD-CURRENT:

Refresh Waterfox
Start fresh to fix problems and restore performance.
This will:
- remove your add-ons and customisations
- restore your browser settings to their defaults
[[Cancel]] [Refresh Waterfox]
Extensions, user styles, plug-ins, dictionaries and languages are (loosely speaking) not removed. I love the convenience, the preservation.
An example, before and after refreshment:



Side note: the third screenshot – all pages failing to load – is symptomatic of e10s: multiprocess enabled with incompatible add-ons after refreshing waterfox 56.0.3 · Issue #380 · MrAlex94/Waterfox.
Change the wording in the dialogue, to not suggest that add-ons will be removed.
From today's Waterfox's current status …:
The
Refreshbutton has been fixed inabout:support. You will now be able to reset your profiles while keeping only your important data (same as Firefox).
To clarify: will the fix cause refreshment to remove add-ons from a Waterfox profile (same as Firefox 56.0.2 and Firefox Quantum)?
@MrAlex94 please advise – thanks.
No it won’t remove extensions, but it may reset their preferences.
Sane. Excellent! Thanks.
I can probably do PRs for basic issues such as this. (I'll wait until after your offline commits go online, then try to find my way around …)
56.2.0, build 20180514223240:

That's enough for me to close this issue.
For other issues with the two Refresh Waterfox dialogues, over to:
Most helpful comment
No it won’t remove extensions, but it may reset their preferences.