Hmm... yes, it isn't really "modifing" the Conky installation. It only changes a Shellscript from Conky as soon as you enable Conky Layout Switcher. (but it reverts this changes as soon as you disable Conky Layout Switcher) - perhaps my post was not clear enought. I tried to ensure that user modified config files will not get deleted and I hope this works definitifly. (it's a lot of work if you modify this files yourself before)

BUT my Application depends on the Conky-N900 package, not Conky. There is a note in the package info at the application manager. So if you have not already installed Conky-N900 on your Device this application will install it together with a special font it needs to work. I don't know what Conky-N900 does with your Conky installation if you have only the old package installed.

Please open the Terminal type conky and post here what happens. Perhaps we could see what isn't working.