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Summary says it all.
Colors remembered correctly. Only changes in font are lost.
To reproduce: go to Tools/Options/Fonts&Colors, select Java, select Method and change the font not to be bold. Confirm the Options. When the file is reparsed, the methods should not longer be bold. Restart the IDE - after initial scan, the methods will be bold again. I do not think there is anything java/editor could do wrong, it seems more like incorrect serialization/deserialization of colorings to me.
*** This issue has been marked as a duplicate of 103247 ***