If both phones were using the same Apple ID, and you enabled iCloud Photos on both of them, that would have merged all of the photos from both phones into one large library – assuming you had enough space in iCloud.
Photos from one phone might be harder to find in the larger library, but as I understand things, simply enabling iCloud Photos in both places would not have caused them to be deleted.
You may want to check to see
- If you are out of iCloud space – if so, you may need to subscribe to a iCloud+ plan with more iCloud storage.
- If you are out of device storage on either the iPhone 6 or the iPhone 6s – if so, you may want to turn on the "Optimize iPhone Storage" setting, giving the phone permission to store local, lower-quality, space-saving versions of your photos and videos.