Produce contents of index with existing directory as cache

Is there a variant of “git checkout-index” which will produce the existing index contents, like “git checkout-index” would do with an empty directory, but can reuse an existing directory tree, to avoid writing all files from scratch?

I'm writing some analysis scripts which need to change a checked-out working tree. Right now I'm throwing away the tree after making the changes and create the next tree (which is expected to be quite similar in contents) from scratch, starting with an empty directory. This is quite slow.

Thanks, Florian