Use the worldedit mod to delete it.
https://forum.minetest.net/viewtopic.php?id=572Sign into your server, give yourself full access: /grant singleplayer all
Next to two opposite sides of the offending block (O), place something like yellow wool or something else you can easily see (X), as close to the offending block as possible. There'll probably still be some space (-) between the offending block and the ones you placed. Something like this, as seen from above: X - - O - - - - - X
Execute: //p set
Click once on each of the two blocks (X) you just placed. They'll be highlighted with "[1]" and "[2]". E.g. they'll look like this: [1] - - O - - - - - [2]
Execute: //set air
Execute: //fixlight
This will usually work for any other thing you need to delete from your map, large or small.