Thank you Ron and Christian for the suggestions! I’ll give both a try. Will the map solution cause BaseX to hold every item from both databases in memory?

It’s just references to the database nodes. To learn more about the memory consumption of particular operations, you can attach a profile function call to map:merge and check out the output in the info view panel of the GUI (or see what the command line returns):

let $originalDB.map := map:merge(
  for $entry in $originalDB
  return map:entry($entry/@id, $entry)
) => prof:memory()