These characters seem to be hardcoded (source).
You could fork the repo and change this behavior or you could use some sort of command line utility on the converted file to remove every line where the #+
characters exist and any other unnecessary newlines.
Let's say we have a notebook that looks like this:

This will be converted to this:
#+
#+
print("print from cell 2")
#+
print("print from cell 3")
We could use a tool like sed
to delete all lines that start with #+
using:
sed '/^#+/d' file.jl
This returns:
print("print from cell 2")
print("print from cell 3")
There are still a lot of newlines so we could use cat -s
on this output:
-s, --squeeze-blank
suppress repeated empty output lines
sed '/^#+/d' file.jl | cat -s
Which returns:
print("print from cell 2")
print("print from cell 3")
We can overwrite the content of the file with this output:
sed '/^#+/d' file.jl | cat -s > file.jl
If you're on Windows and you don't have a sed like utility installed that you could apply above idea with, you could look at this post.