As previously noted, Patch 1.02 (equivalent to 1.0.5 on PC) released for PS4 versions of Enter the Gungeon resulted in unforeseen consequences. Almost immediately after the patch was certified and pushed live, some issues were identified that caused save file loading failure for certain players. In response, the patch was rolled back to 1.01 (equivalent to 1.0.0 on PC).
The good news is that your save has not disappeared. The save is still there, it's just not being read by the game client. A new patch (1.03) is currently in development that should rectify that. Thankfully, there are also plans to save not only your old saves, but your progress made in 1.02. In the new patch, your progress on the glitched build will be copied to Slot D, with your original saves copied to Slots A, B and C.
It might feel like you're losing your progress when 1.03 drops, but you will simply be reverting back to your original saves. Your save from 1.02 will be intact, however.
More updates to come as the patch is certified and pushed out.