Unfortunately, the books were deleted when you deleted the app; you'll have to get them back in the app the way you got them there the first time.
If you made a backup in iTunes just before deleting the app, those books may be (repeat, MAY be) in the backup for that app. So, you can try connecting your iPad to iTunes and selecting "restore from backup." This will put that backup onto the iPad.
Just know that the backup will put your iPad back to the state it was in at the time of the backup - which may be old and outdated.
The easiest thing may be to find and re-load your ebooks....
Marilyn