Have you tried reselecting to filter out the bottom holes before the join.
Question, is the data structure the same for the two files? If they are, can you just recreated/export to a new shapefile? If you need those bottom holes added back, you could alwas put those to a temp file and then append them back on. If not, and you only need the 19k points, but need to keep them in sync, maybe think about setting up a one-way replication.
Replication types—ArcGIS Help | ArcGIS for Desktop
Just trying to give some alternatives that might be easier...of course depending on what you need as the finale.