Inferring bond breakage in a reaction from InChI strings of reactans?
There is the Reaction Decoder Tool (RDT on github) that can - from the README - do:


  
  Reaction Annotator (Extract Bond Changes, Identify &amp; Mark Reaction Centres)
  


EDIT: It potentially could have InChI support, but a quick glance at this file suggests that it currently doesn't...

In fact, that would require the CDK/RDT to implement the rInChI format

The input formats includes reaction smiles which should be possible to generate from your smiles strings. Looks like you just jam a ">" inbetween reactants and products with a "." separating the molecules in each set.

which sounds like what you want, I think. Also it should be able to handle those volumes as it has been developed to work with reaction databases at the EBI.

(Full disclosure : I worked on the project for a little while :) but it does have InChI support  - via the CDK).