If you're using the iCloud sync feature, whenever the Apple's iCloud mechanism clears the iCloud Cache, the book needs to be downloaded again in the app. We actually do not have any control over the timing aspect of this iCloud cache clearing mechanism by Apple.
If you keep your books locally and use the Dropbox/OneDrive/Google Drive auto backup features instead of the iCloud then, the books will always be available on your iPad.
We're working with Apple on this to see if there's a better way to handle this method. Kindly bear with us on this one.
UPDATE (JUN 2021):
We did some changes & workarounds in this area. In order to fix the graying out issue that we had earlier, we are now storing them in a temporary location. If there is less free space on the device or if the app is deleted, these caches will also be deleted. So the only way is to re-download them again.
Always ensure you have enough free space on your device (at least twice the amount of the app's size) & iCloud account to avoid such issues.