Since 3.6, vanilla Stellaris has had a bug with synthetic assimilation: assimilated pops are converted into the undeletable founder species instead of the latest modification of that species. Since Total Assimilation functions similarly to synthetic assimilation, it has the same issue.

When Paradox fixes it for synthetic assimilation in the base game, it should be automatically fixed for Total Assimilation. Until then, you can use one of two workarounds:

1. Every so often while Total Assimilating pops, run another species modification project to convert the unmodified species to your latest modification of the species. You can choose how often you want to do this, based off of how much assimilation you're doing and how bad your unmodified species is.
   
2. Each time you modify your founder species, run the script below in console (press `, paste the script, press enter, press `). This will reassign the dominant species to whichever version of your founder species has the highest population. This makes your game invalid for achievements.

Here's the command for option 2:

Thanks to Zargachi, Adohleas, Dr. Nolegs, and Reianor for figuring all of this out.