Why does my custom WordPress plugin’s directories get merged (not overwritten)?

I created a custom plugin for my site that handles things like loading custom css files, and modifying output server-side. I use Local by Flywheel for local site development and AllInOneWPMigration for moving sites.

When I export and import a site, use the “find and replace” function in AI1WPM and export to a file. I then upload using the same plugin on the other site. I notice that my custom plugin’s directory structure changes on import. Instead of my plugin directories and files being overwritten with the new directories and files, my directories are being merged. The files with with the same name are properly overwritten with the new file, but all other directories and files are combined.

Why is Local OR AI1WPM merging these files, as opposed to overwriting/replacing my custom plugin’s files/directories?