I had applied for a c.o.s. from F2- H4 visa and I had not got the approval yet.In the mean time I decied to join a school to do my masters.I had got my I-20 from the school also,I have not yet filed for another c.o.s. nor have I paid the SEVIS fees.
Will taking a I-20 from a school hamper my pending c.o.s. from F2-H4?

If you want to be on F-1, submit a letter to USCIS and cancel your H-4. Then apply for F-1, pay the fees, etc.
You can also go to school on H-4 but won't be eligible for CPT or OPT.