I just updated Cydia substrate PAM modules and shell-cmds and I can still see and use Tiny Mod (although I'm still on iOS 8).



There are several steps you can take to possibly fix it.



1. Disable/Uncheck the theme, respring and re-enable the theme.



2. Make sure you are applying the right theme. (LS Barebones - Tiny Mod is installed to /LockHTML, /GroovyLock, and /SBHTML so it may be showing one or two different versions.)



3. Re-install the theme or uninstall, respring, and re-install.



4. Install the tweak "Nella" and rollback the updates by going to the updated tweaks, tap modify and select "Downgrade".



Hope these help.