You will be eligible to receive an ITA under FSW/CEC/any other PNP until you receive and accept a nomination from Ontario. The only flip side is that you will lose 1500 CAD by withdrawing the nomination application.
From this link...
http://www.ontarioimmigration.ca/en/pnp/OI_PNP_EE_CAPITAL_FAQ.html
I provided my application for nomination to Ontario and paid the appropriate fees. I recently received an Invitation to Apply (ITA) from the federal government. What do I do?
If you wish to proceed with the ITA and withdraw your application for nomination you must notify MCIIT (see Q.13 on withdrawing an application).
Also, hope you understand the broad timelines under OOPNP.
1. You have
45 days to accept/reject the nomination. Accepting a nomination entails filling up and submitting the form along with a
non-refundable fee of 1500 CAD. Actually, the fee is refundable if they reject your application as incomplete but non-refundable otherwise.
2. Under the program, MCIIT will process
80% of applications within 90 days. If your application is processed positively, you will receive notification about the nomination in your MyCIC account
3. You have
30 days to accept or reject the nomination. If you accept it, 600 points get credited to your account. With those additional 600 points, you will get an ITA in the very next draw (within
60 days assuming they do at least 1 draw every month).
4. After receiving an ITA, you have
60 days to accept or reject it. Accepting entails submitting all required documentation and paying the required fees.
5. Finally, CIC will process 80% of all applications within
6 months of submission. If your application is processed positively, you will receive your PR.
All the best!