We had some issue with Lucene not indexing properly. Usually with the removal of the indexes folder within data folder and rebuilding the indexes through Control Panel's Indexing Manager helps; however, do people generally remove the indexes folder and rebuild indexes manually? What will be the best practice to help regulate performance of Lucene and indexing.
From what I remember if you perform a full index rebuild from the Control Panel, index files will be removed. You don't need to do this manually.
And yes, sometimes indexes may become corrupted for multiple reason. Like network connectivity issues or application restart. Rebuilding the whole index may be the easiest option in some cases.