Oh, I see what happened - my development directory has a bit of cruft (including an old eyefi-config.h) left in it, so I didn't notice that there still was a reference to the old file. Thanks for the catch.
In any case, I'm fairly sure the sha1 and md5 files aren't actually used yet, so you might get away with just removing them.
I removed them and now I have this error.
../lib/eyefi/libeyefi.a(eyefi.o): In function `make_network_key':
eyefi.c:(.text+0x274): undefined reference to `pbkdf2_sha1'
../lib/eyefi/libeyefi.a(eyefi.o): In function `fetch_card_key':
eyefi.c:(.text+0x6c0): undefined reference to `memmove'
../lib/eyefi/libeyefi.a(eyefi.o): In function `fetch_card_firmware_info':
eyefi.c:(.text+0x6f8): undefined reference to `memmove'
../lib/eyefi/libeyefi.a(eyefi.o): In function `fetch_card_mac_address':
eyefi.c:(.text+0x728): undefined reference to `memmove'
collect2: ld returned 1 exit status
So SHA1 is definitely used but what is memmove?
Do you still have your working copy and can you upload the whole copy to a file share site?