Your issue is an upgrade problem and has nothing to do with the problem described here causing damaged uedit32.ini in previous versions (exactly v13.00+5 to v13.10a+2) in special situations.
An upgrade from v12 of UE to v13.20 should be done without any loss of config settings. I tried it and it worked well. Well, I don't have any FTP accounts set and so don't know how they are converted after first run after installing the new version.
Menus and toolbars could be automtically re-created. If you have customized a default menu or toolbar profile (Advanced or Basic) then you always must take care at first start after an upgrade. UltraEdit has 2 versions entries in the uedit32.ini for the standard menu and toolbar profiles and when it detects on start, that they doesn't match with the internal version for the profiles in the EXE, UltraEdit asks you if you want to update the menu and/or toolbar profiles and if so create backups. I use the standard Advanced menus without modification, but customized toolbars which I have created using "manage toolbars" and saved with different names. So I always can agree to update the 2 standard menu and toolbar profiles without a backup and without having the fear to loose my customized toolbars. At How to update the menus and toolbars?
I have explained step by step how to setup such a configuration.
Look in the folder with uedit32.ini if there are backups of your previous menu and toolbar profiles which you could restore using manage menus/toolbars.
Other configuration settings like the font used should not be changed by an upgrade. A possible reason for a font change could be Configuration - File Handling - Code Page Detection
It's also possible that you specified in the previous version to use the registry for settings and now you use the INI. Then you would need to set again to use the registry. That setting should not change automatically, but I have never stored settings in the registry, so I don't know how this configuration is handled.
To your last question: Can I get back my settings?
Yes, if you have made backups of the configuration files before upgrade which I always do, not only for IDM products, for all programs I use (mainly because I want to know what's new after an upgrade and first run and not because it is dangerous to upgrade).