1) Can the police withheld my Passport and deny travelling back to US? If yes, what all thing I can do to avoid this?
Police Has got no power or right to seize of withhold your passport, they may insist on submission of passport to them, you keep dodging the submission because once submitted, they will deposit it in the court which will become difficult for you to retrieve it.
2) I have a very strong case and all her allegation can be proved baseless, which the police also know. Can someone file a 498A after almost 1 year of divorce petition?
Yes there is nothing wrong in filing a case after one year too because it is a continuous offence.
3) I have a property on which me and my wife both are co-owner but i have been paying all the EMI's. I have asked her time and again to return back the ownership of the property.But she didn't? Now when the police come to seized all the belonging which i wife got can i ask them to return the property ownership? (FYI- my wife has taken all her jewelleries from my house without my permission long time back)
There is nothing wrong in she taking her jewels back, it is legal and valid, and she doesn't have to inform you or take your permission for doing so. But in the property jointly owned by you and her, you cannot force her to give it back to you because the fifty percent share in the property belongs to her and she is the absolute owner of the same which you cannot deny and it would be illegal and offendable.