I followed instructions an uninstalled .49 and then installed .54. I did not opt to blow away decks.
When I opened .54 it showed 2 profiles instead of the 5 previously available. When I looked for add-ons, I found none. The addons and addons21 folders have not been deleted and appear to contain their original contents.
If the add-ons don’t work on newer versions, they may have been automatically disabled. Profiles disappearing sounds like you might just have a problem with your config file - you could check your Anki data folder to locate the other profile folders.