Just a follow up if anyone is interested.

Cherry: Not needed
As I have never been interested in that service anyway: No reinstall.

microb-geolocation: optional
I might need it with microB. Since it doesn't harm and has not been removed on purpose: Reinstalled.

osso-startup-wizard: optional
Helps with setup stuff like language and datetime. Since I won't change that anymore, I don't need it at the moment. Besides I won't get bugged by it, when restarting after having batteries removed: No reinstall

rtcom-accounts-voip-support: Needed
My SIP account wouldn't work without: Reinstall.

libtheora0, libvorbisenc2 and tracker-extractor-vorbis: unsure
Still no idea, If they are removed by update Ogg Support 1.1.1. If so I might not need them.

btw: the modest-home-applet disappeared once more a few days after the first incident. Had to reinstall again. I am almost certain that I didn't install any other software in between those.