I'm afraid the file structure is not layd open for all users, but you will have a good chance when you ask Cypress directly.
At top of this page Support & Community -> Technical Support -> Create a MyCase and leave the relevant information there. A Cypress engineer will get in contact with you.
Just a remark from my side:
Usually this is done just the other way round: You keep the pins fixed after the first successful routing in Eagle and when necessary, change the internal connections, so that a pcb re-route is not needed. This will work pretty well for PSoC5 and 3, only the PSoC4 has some limited routing capabilities where this way may lead into some troubles.
There is one caveat here, if you are doing Analog.
You need to be very careful when routing the Analog signals to the PSoC 5 pins. If you route them through the crossbar matrix, and not directly to their "natural" outputs, you will get dramatic cutoff frequency drop.
Based on my tests, Opamps do very poorly with signals as low as 20khz when routed through the crossbar.
In PSoC Creator, there is an analog tab at the bottom of the CYDWR sheet that will inform you of the analog components being used, and where they are routed. Very useful.
"Currently, PSoC Creator doesn't support to export pin information to some external file.
However, I have filed internal enhancement report to add this feature in future version of PSoC Creator."
@wsm, what you say about the analog thing might be relevant to me, since I am trying to use a 5-way analog mux into an SAR, currently on P2. This note indicates that I should switch that to P0, P3, or P4: http://www.cypress.com/?docID=49602
This is where the described tool would be useful! Rotate the chip in the design 90 degrees and then auto-regen all the new outputs, going in either direction, Eagle <--> Creator.