Reinstalling everything should fix this.
Timer service is a system app (i.e. an internal appserver app) and as such is deployed once on the 1st server startup. You can't redeploy or undeploy a system app. The timer application is implemented using CMP and during deployment the CMP impls and other artifacts are created under the generated area. When you removed some of the generated direcories, you broke the timer app, but even if you don't need it, it's registered with the app server, and being started to be ready to use on the server restart.
HTH,
-marina
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