[Haudek]

Try this.

Spoiler:

import re
from sigil_bs4 import BeautifulSoup

def run(bk):
    PageNumbers = r'(\d+)(?=</a>)'

    for (id, href) in bk.text_iter():
        print('Processing:', href)
        html = bk.readfile(id)
        soup = BeautifulSoup(html, 'html.parser')

        modified = False

        for p in soup.find_all('p', class_='inp'):
            i = 0  # HERE RESET

            def IncrementalNumbers(m):
                nonlocal i
                i += 1
                return str(i)

            new_html = re.sub(PageNumbers, IncrementalNumbers, str(p), count=0)

            if new_html != str(p):
                modified = True
                p.replace_with(BeautifulSoup(new_html, 'html.parser'))

        if modified:
            print("Modified File -->", id)
            bk.writefile(id, str(soup))

    return 0

def main():
    print("I reached main when I should not have\n")
    return -1

if __name__ == "__main__":
    sys.exit(main())

Look at line with "RESET HERE". Here we reset the counter and each paragraph is counted separately.