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Ace3 (not ACE3, it isn't an acronym) via AceDB only saves changes if the user actually makes a change. Say you have a default of "pet" = "dog". You will see nothing in the SV file for that entry. Should the user change "pet" = "cat" then you will see MyAddOnDB.profile.pet = "cat" in the SV file.
Changing the contents of the default table on the fly won't always change because the previous data is still in memory, as you discovered. You might have to completely exit the game to test. You can add to the table and reload, but removing entries from the table might not work as intended without a complete restart.
What do you mean by an "empty state"? And in your OnItialize() function you specify RaidSummonSyncDB = {} on top of self.db = LibStub("AceDB-3.0"):New("RaidSummonOptionsDB", defaults, true). Why are you setting up two saved variables, one without AceDB? For that matter, line 223 tells the addon to wipe RaidSummonSyncDB each time it is loaded.
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