Injustice 2's newest patch, released today, is designed to fix September 26's patch that had a nasty habit of deleting players shaders, virtual currency, and unlocked gear.
The September 26 patch, updating the game to version 1.10, immediately resulted in players reporting missing items from their save files. This can be especially annoying for players as the gear is not easily obtained again, as it is randomly doled out through loot crates. After the patch, those items just simply disappeared.
NetherRealm acknowledged the problem, but did not have many solutions beyond rebooting the game until this patch. While the patch seemingly puts an end to the item deletion problems, it does not restore anything for some players who have lost their items already. Strangely, it has helped some, making it harder to determine the problem or for players to figure out what works.
If you never updated to last week's 1.10 patch, you're totally fine to update now. If you did, hopefully you're not one of the affected players, or that NetherRealm has a solution in the pipeline.