For the benefit of future readers:-

@Toto's answer may replace other numbers as well, so I am posting another PythonScript here to match <sup>, followed by a [ bracket and then the number sought as per the question. You can run a python script within the PythonScript plugin of Notepad++ for that.

If it is not yet installed, install it via Plugins Admin. To install the PythonScript plugin in Notepad++, navigate to Plugins > Plugins Admin. Check the box next to PythonScript and click Install. Notepad++ will restart, and after that, you can find the plugin in the Plugins menu.

• Create a script (Plugins >> PythonScript >> New Script)

• Copy this code and save the file (for example increment.py):

# encoding=utf-8
from Npp import *

def custom_replace_func(m):
    new_text = "<sup>\[{}".format(custom_replace_func.counter)
    custom_replace_func.counter += custom_replace_func.increment
    return new_text

custom_replace_func.counter = 1  # starting value
custom_replace_func.increment = 1
editor.rereplace(r'<sup>\[(\d+)', custom_replace_func)

• Open the file you want to modify

• Run the script (Plugins >> PythonScript >> Scripts >> increment)

• Then, in the result obtained after the above, put the cursor before the first <sup> and hit Ctrl+H and in the pop-up, type <sup>.*?\[ in the "Find" field and <sup>[ in the "Replace with" field and hit “Replace all” to get rid of the \ after every <sup>