Can’t you just replace the tokens before converting them to IDs?
# set of all tokens that should you be replaced
NEED_REPL = {"##না"}

def retokenize(tokens):
    return [t.replace("##", "", 1) if t in NEED_REPL else t for t in tokens]


tokens = ['আ', '##জ', '##কে', 'হবে', '##না']
replaced = retokenize(tokens)
print(replaced)
# ['আ', '##জ', '##কে', 'হবে', 'না']