updating database

We have a knowledge base that needs updated every night from a text file.
Currently a script deletes everything from a table and adds the new data.
This procedure seems to slowly cause the database to loose performance
daily.  It also leaves our database useless for several hours starting at
midnight.  I thought about using 2 databases, updating one while using the
other, then swapping them every day.  I also thought about having one
db.out, then the other in.

Is there a better way to do this?

Thanks in advance.

Charles Day