Themes are located in a path associated to the ACLI shell app in your user home. The exact location can be viewed as part of the themes documentation available using the /settings themes slash command. The bundled files in this directory may be overwritten with the installation of new ACLI versions.
If you want to create a customized theme, it is recommended that you copy one of the bundled themes to a new file and modify to create a custom color scheme to your liking. It is strongly advised that you do not make modifications to existing themes.
ACLI Shell HTML Style Guide - advanced theme customization information