Как я могу использовать регулярное выражение, чтобы получить строку внутри двух символов и удалить определенные символы внутри этой строки

Вы можете отфильтровать непечатаемые символы:

import re 
from string import printable

# your invisibles are in the string...

s='''<@961483653468439706> Text to remove, this text is useless, that's why i want it gone!
Type `keep the letters and spaces` and `this too`'''

for m in re.findall(r'`([^`]*)`', s):
    print(repr(m))
    print(''.join([c for c in m if c in printable]))
    print()

Отпечатки:

'k\ufeffe\ufeffe\ufeffp\ufeff \ufefft\ufeffh\ufeffe\ufeff \ufeffl\ufeffe\ufefft\ufefft\ufeffe\ufeffr\ufeffs a\ufeffn\ufeffd s\ufeffp\ufeffa\ufeffc\ufeffe\ufeffs'
keep the letters and spaces

'this too'
this too

Вам не нужно использовать регулярное выражение для этого:

text = "<@961483653468439706> Text to remove, this text is useless, that's " \
       "why i want it gone!Type `keep the letters and spaces`"

# put your invisible character between the first quotation marks here. obviously, they
# don't show up in this post.
filtered = text.replace('', '')
# because the passage you want is always between ``, you can split it and know that every
# second item in the list that split returns must be what you are looking for. 
passage = filtered.split('`')[::2]

print(passage)