I have a QuestDatabase.json in a save file from before the quest progress was kept in a separate file. Attempting to load that save wipes my questbook.

The DefaultQuests.json in the config directory has changed since that save file was made. Will I need to manually update my QuestDatabase.json before the progress will be imported properly?
I'm attempting to upgrade to 1.0.124, though this also occurred in 1.0.121 and a couple of versions prior to that. In Minecraft 1.7.10.

Just to clarify but by wiping do you mean it deletes all the quests completely or just the progress and completion data associated with them?

The progress and completion data.