Oh yeah, i've encountered this issue before. Basically, when you upload your vanilla world to aternos's paperMC software, the world is converted to 3 diffent folders (world, world-nether, world-the-end). The DIM1 folder from the vanilla world is supposed to be moved to world-the-end folder but instead renamed to DIM-1 and then moved to world-the-end. That is the reason your end dimension got reset. You could fix it by download your world-the-end folder, extract it, delete the DIM1 folder inside it and rename the DIM-1 folder to DIM1. And then reupload it onto Aternos
Im not sure this is an aternos bug or paperMC bug Roman humoodiplayz