Considering the replacement cost and lead time of two speed 900 HP motors, don't go cheap on protection.

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Ohm's law
Not just a good idea;
It's the LAW!

The SEL (Schweitzer) 710 MPR has the ability to protect 2 speed motors. It holds the protection profiles for each speed in its memory. You would then just put one set of CTs up stream of the contactors and give it an input to tell the relay which speed you are running at.

" We are all here on earth to help others; what on earth the others are here for I don't know." -- W. H. Auden

All the modern motor protection relays available in the market can hold multiple groups of settings those can be switched using a binary input (BI).
I guess you can program the relay settings - one group for one speed and switch them using an auxiliary contact (from speed changing contactors) wired to the relay as BI.
I am not sure whether the CT input can be configured separately for each group of settings in these relays (needs to be looked in to further).

Thinking back to an off the wall revenue metering connection, that worked well as long as voltages were balanced;
I don't think that you the CTs in series.
A Blondel solution requires N-1 meter elements in relation to the number of lines.
ie: A delta circuit or a three wire wye circuit (a motor circuit) requires two meter elements for accurate metering.
A four wire wye circuit (line to neutral loads) requires three meter elements for accurate metering.
I was faced with metering an industrial load (About $100,000 per year billing) with only two element meters available.
One element metered "A" phase.
One element metered "B" phase.
The vector depiction showed an open delta connection of the CTs.
The third CT for "C" phase was connected in delta.
The ratio of impedances between the meter elements and CT secondaries is very high and the output current from the "C" phase CT is forced through the meter elements for "A" phase and "B" phase.
Each phase contains components of the other two phases.
Thus the "A" phase meter element measured the "A" phase component of "C" phase and the "B" phase meter element measured the "B" phase component of "C" phase.
The circuit is published in a recognized metering hand book. (Published by either Westinghouse or GE. Memory fails.)
I was skeptical, but hidden single phase check-meters running for a few months verified that the connection was metering accurately.
In you situation:
For a two winding motor, the CTs may be connected in parallel.
For a consequent pole motor, rather than metering the supply lines, meter a set of windings that has the same current whether running in high speed or slow speed.
It may be possible to meter with CTs in the leads to the shorting contactor.
Note on non-Blondel metering solutions.
Did you realize that all of the hundreds of millions of single phase, 120/240 revenue meters in North America use a non-Blondel solution?
The common North American revenue meters assume that the line to neutral voltages are equal.
When an unbalance loads cause a voltage drops in the neutral supply conductor, the metering becomes inaccurate. (But close enough. The slight error is in the favour of the utility. Want to try a class action suit? I am sure that the utility will argue that the error is offset by the extra un-metered I²R losses in the neutral conductor caused by your unbalanced load.)

--------------------
Ohm's law
Not just a good idea;
It's the LAW!

GE 869 is not the answer.

Link 

Any SEL or GE Multilin motor relay can do this. You only use one set of CTs so move the high speed CTs to be ahead of the switching contactors or install new CTs. You'd have to really hate money to want a relay that can use two sets of CTs.

Quote:

GE 869 is not the answer.

So what if an old version of firmware is obsolete? The relay is still very much in production and will be for many years since it was just recently released.

Yes, it is possible to program a relay for two current settings. You can provide digital inputs to relay for speed 1 & speed 2. The relay will see the current as per the speed input.