Eligibility is based on 'the date of submission of the programme (Art. 65(2) CPR).
If the Operational Programme was submitted on the 5th of October then the eligibility will remain this one since a new working version is a re-submission.
For example:
Version 2.0 is sent to the EC on 05/10/2017.
Version 2.1 is sent to the EC on 01/11/2017.
Eligibility date = 05/10/2017