yEd stores user settings in its profile directory. (Palette settings specifically are stored in the palettes sub-directory of the profile directory.) The profile directory is separate from the yEd installation directory. The yEd installers do not change/modify the profile directory in any way when you upgrade your yEd installation. Actually, the profile directory is not even removed when you uninstall yEd.
In short, upgrading should not affect your palette settings.
The only two reason I can think of for losing your custom palette sections are:
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You removed yEd's profile directory.
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You explicitly changed yEd's profile directory (either for the old or for the new version) and yEd is now using a different profile directory than before (and thus has no access to your previous settings).
In the first case, there is nothing that can be done about it. In the second case, you can restore your settings by copying the old profile directory to the new profile directory.
