Probably you did. I can not be 100% sure but my core voltage was 0.5 like yours when they were 0 kohm each...being 3 kohm each it means that you should get very high VCC core (my oppinion) voltage or something else around is damaged which shall be the case
Try the wire thing as suggested. As stated PCB is easy to damage. If you happen to fix at least one of the cores you will able to measure correct core voltage
There are always better solutions (routing/VHDL/Verilog/partitioning optimizations)
Really no one should be playing with the core voltage, UNLESS they have enabled both in-chip/external temp and external current measurement.
Problem is that such things that allow you to fiddle with the core voltage vary significantly from batch to batch & the age of the Chip.
You will find that current and internal die temp start to show signs that you are getting close to the danger zone, whilst you still have time to back them off.
Certainly making mods to a small group of FPGA then retroactively applying the 'fix' to masses of production out in the field, really is only going to end one way, plus such damage is really going to F*** any chances of returning the units for trade in.
The question should be:
Is the mod going to make more bit coins between now and trade in, than the trade in value of the device?
If not then leave it the F*** ALONE!!!