The game will load the player back at the last checkpoint, but the boss will stay defeated. Instead, save and quit, then restart the game. After beating the boss of the game's first vault and unlocking the Eridium artifact, players should not progress the Beneath the Meridian mission any further.
The most efficient method to farm Eridium, however, is one that most players will likely miss. These enemy types have a greater chance at dropping money and Eridium, so players could easily reload zones to continually farm these encounters.
Leaving a zone often results in Borderlands 3 respawning enemies, which also includes powerful ones.