I just limited my four month old daughters pacifier time. Now she has started using her thumb. What should I do ?

Sorry, but if you had to limit the use of pacifier in her fourth month only, you should not have introduced it to her in the first place. Anyway, if she has started sucking thumb, then either you put mitten or let her use pacifier for a few more months, as it is easy to get her off pacifier than thumb.