After enabling WPML a lot of the media we had in our media library vanished. The count when from near 14k records to 4k. After disabling wpml it went back up to 12k but many of them appear to be duplicates of each other.
UPDATE: I see that I may not have lost a lot of images, but we are definitely seeing something strange. On our dev site, it shows 14k images with wpml enabled. I see that the the media library is showing up to 5 records for each image with wpml enabled. This led me to believe our original media count was much higher. On production it seems to be grouping the images together causing the count to be closer to 4k. Can you please provide a link to documentation on how the media library is expected to work with wpml enabled.
Activating the WPML plugin should not remove any images from your media library. What you're encountering seems to be isolated to your side for some reason.
If you check the media library, there is a language switcher on the top of the admin bar which allows you to switch between languages and show the image that belongs to a certain language.