Alpeshji,
In my humble opinion, whereas legal validity of the document cannot be questioned, however stamping is to be done on or after the date of execution, not before, except in case of Foreign Documents which can be stamped within 3 months after their arrival in India. This is on a reading of the Karnataka Stamp Act, and I'm sure Bombay Stamp Act also has some provisions in those lines.
The consequences of non-stamping are that, any legal or quasi-judicial authority before whom the document is produced must impound it, and the document will be legally valid only on it being adjudicated by the District Collector and penalty paid as per relevant Stamp Laws.
To prevent this, it would have been better to go in for an adjudication and paying penalty for the delay with the Collector before franking the stamp duty on the instrument.
It depends on what you are filing. Is it related to filing returns of allotment for consideration other than cash? Is it related to Charge Registration? Based on the type of document, a strategy will need to be devised. If it is an STP form, ROC will never come to know of it unless triggers or threshold limits are crossed, in which case scrutiny will be involved.
If it is an ROC approval form, as you said you can wait for the ROC's opinion in the matter.
Do keep us posted, and kindly give further details to the extent confidentiality permits.
-Ulhas