Dear shruti,
the compounding of offence does not relives from default in filling documents, return etc. so even after the offence is compounded the company is under obligation to file the same.
as far the period of three years is concerned the provision, i think is only that and i quote: "...offence committed by company after the expiry of the period of three years from the date on which a similar offence committed by it or him was compounded under..."
regards