The Muslim proportion in "undivided India" - today's India, Pakistan and Bangladesh - has risen from 21% in the late 19th century to about 31½% today, but there can be little doubt that the rate of increase was slower in the C19, much of the 20th-century growth being concentrated in the area now forming Pakistan which saw exceptional agricultural development from the 1880s. This is consistent with experience elsewhere: past populations were on the whole less mobile and less subject to rapid economic transformation than in recent times.
A tentative reconstruction for c.1850 based on McEvedy's breakdown into today's areas (Atlas of world population history, Penguin 1978) suggests about 11 million Muslims in what is now Pakistan, 23m in today's India and 15m in Bangladesh (against 15m, 29m and 19m respectively in 1901) - in all roughly a fifth. In 1800 with a total population of 190-200m we're probably looking at a Muslim contribution of 35-40 million (about a fifth of them in Pakistan, a half in India and 30% in Bangladesh) as there is no reason to assume any disproportionate advance in areas of predominantly Muslim settlement. It's certainly a good deal more than 25m or the first source's 13%, numbers derived from extending 20th-century trends into the 19th where they simply don't apply.
Of the three present-day states, Bangladesh has shown the least change in its share of the subcontinent's Muslim population, rising to 32% in the 1960s before falling back to 27% today: population movements at the time of partition raised Pakistan's share from under a quarter to more than a third while lowering India's from 45% to 35%: today Pakistan and India each contribute 36-37%.