Yes Sir. I am well aware with this incident which had happened with you. As per official notifications, change of boarding point would not affect any quota distribution.
For example:
A-B-C-D
Let's say I wish to travel from B-D. Due to unavailability of tickets from B, I purchase a confirmed/RAC/WL'ed ticket from A-D.
Now...
more... if I change my boarding point from A to B, the initial quota allocated to me would remain the same. Even if I have a WL'ed/RAC Ticket, the quota allotted would remain the same and any cancellation/confirmation matrix would be calculated by taking my boarding point as A.
In any case, I am paying the full fare from A-C.
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It has been often noticed that such disputes regarding change of boarding point is prevalent mostly to trains plying from/to Southern Part of India.