You can update the games manually with this installer.
You can't update your console to 5.5.0 (because it will think you already are on 5.5.0) and you can't downgrade the "spoof" to tell the console you are in fact 5.3.2
so if a game requires a file that was installed on a 5.5.0 update, it will miss it. (currently, no game requires specific files added after 5.3.2 so you are fine, but nintendo might start requesting checks added in next/future updates to prevent spoofing without updating all files)
If you want to add missing 5.4.0 and 5.5.0 files, on next update (5.6.0) you should be able to install them by updating officially (but you will lose your hacks capability)
the official update checks all your current installed file versions and update the outdated one. it's not only updating a fixed list of file so the missing files (from 5.3.2->5.5.0 spoof) will be added when installing 5.6.0 (5.3.2->5.6.0)
as the console looks like it's on 5.5.0, you can launch Mario maker, and probably download levels (if you don't need to go to eshop).
The filtering (DNS or Proxy or router) is used to prevent the console from downloading current/future updates from nintendo's servers.
if nintendo release 5.6.0 or 6.0.0 then the console will update automatically ! to prevent that, you need to block nintendo's servers (and nintendo's IP too for better safety)
There are two guides in the FAQ sections to block update download. one relying on an online filter (DNS) which is not 100% safe and one relying on your computer's filter (Proxy) which is safer than DNS but still not 100%. the other one is not in the FAQ as it's different for every users (Router filter) but it's the safest solution.
Edit:
ZombiU update applied successfully
