Hi Sandip,
Yes those urls should be restricted by robots.txt. Since CDSEO now has the canonical link urls they don't necessarily need to be blocked either though.
Its normal for rankings to flucuate temporarily during the indexing period. Make sure that you installed CDSEO correctly and its working correctly and otherwise don't panic
We've
never had a single person install CDSEO Pro properly and come back to us and say their rankings didn't improve after reindexing.
If your feed manager pro is very old - which it likely is being on 4.0 - its probably configured for CDSEO Basic no pro, so you'll want to upgrade to the latest feed manager version.