>> This may be a stupid question and dont take it wrong,<<

I once heard that the only stupid questions are those that are not asked.

>> But are you dropping all your indexes before you clear the tables and re-add all the data.
Then rebuild your indexes on the fresh data? <<

Yes, but there's more:
1. Build temp table from table definition
2. Import new data provided from outside source
3. Index (answering your question, yes, on fresh data)
4. Rename old table
5. Rename temp table to bring it "live"