The problem stemmed from a simple but critical mix-up: the developers accidentally uploaded a debug build of the game instead of the intended public build. This debug version was configured to look for save files in a different directory than the standard game, which is why your NG+ playthroughs suddenly appeared to be gone.
A Simple Fix for a Scary Bug
Thankfully, the fix was as straightforward as the cause. The correct core game build has now been uploaded for all platforms. Once you update Metal Eden, the game will once again look for your save files in the proper location, restoring access to your NG+ campaigns immediately.
Were my Metal Eden save files deleted?
No, they were not. Reikon Games confirmed that the issue was purely about file recognition. Your saves, whether stored on your PC or in the cloud, were never impacted, deleted, or corrupted. The game simply couldn't see them due to the wrong build being active.
With this issue resolved, HYPER UNITs can jump back into the hostile orbit of MOEBIUS and continue their mission without having to start over. It's a quick resolution for what was undoubtedly a heart-stopping moment for many players deep into their second playthroughs.