is there a way to make levels replace existing levels?
Not at the moment.
maybe just a way to retaxture existing files?
there is an override folder and its rather easy to use! :D
just in game press t and type /dumpsprites, after that a "Dumped" folder will be in your nuclear throne folder, now go into that and find the area floor sprites that you want to change, copy the names and then find the floor sprites you want to change it to
next just rename the floor sprites
like lets say you want to replace the sewer sprites, the floor specifically
instead of using whatever name you had it set to beforehand rename it to "sprFloor2"
then put it into your override folder! and you're done! this can also apply to weapons and characters and other things
wait, into what do i put the dumped folder?
the edited sprites, like lets say you edited "sprMutant6Idle" take your custom sprite into the "override" and then "sprites" folder
after that get up to wherever you meant to and it should work just fine! (areas have a slight problem though)