You can lose a region, if the habitats of your alliance get captured by other alliances. If your share of captured habitats in a region sinks below 80% at a Region Update, you have lost the region and all its bonuses.

Once your alliance controls less than 80% of all habitats in a region at the Region Update, the region status will change to “pending”. You will only fully lose the region if you still do not control enough habitats at the next Region Update.

Once a region changed its owner, all its upgrades are reset. Therefore, whenever you capture a region, even it was yours beforehand, you have to start over upgrading it. 

So make sure you don’t lose control of a region, especially if it is completely developed. On the other hand, you can weaken your enemies heavily when they lose a fully developed region!