That's strange, what version of the daemon where you using previous to the update?
FYI. I'm using your new binaries OK in Win 7 x64. Blockchain sync picked up where it left off. I was using "aeon-phoenix-rc1-win-x86_64.zip" (shows as 0.8.8.2() in the logs). Not sure where I pulled that binary from... maybe was yours too.
same behavior here with cryptrol's build, win7 64, and blockchain bootstrap:
2015-Jul-22 22:13:49.122523 Loading blockchain...
2015-Jul-22 22:13:49.216123 ERROR C:\Users\u\Documents\GitHub\aeon\src\common/boost_serialization_helper.h:108 Exception at [unserialize_obj_from_file], what=unsupported version
2015-Jul-22 22:13:49.231723 Can't load blockchain storage from file, generating genesis block.
i'm testing my own build and under the same conditions, blockchain bootstrap is loading as expected
2015-Jul-22 21:54:33.882682 Loading blockchain...
2015-Jul-22 21:56:58.270948 CHECKPOINT PASSED FOR HEIGHT 1 <1440a20f078bf3264822234b347f8382606577d73d4e9d3cb7296d73889bc421>
2015-Jul-22 21:56:58.629748 CHECKPOINT PASSED FOR HEIGHT 100 <6dd13aaab16679f49ee6b2b75c7dc99b1fd09ab2282b18cb4b55b73110655742>
2015-Jul-22 21:56:58.816949 CHECKPOINT PASSED FOR HEIGHT 1000
2015-Jul-22 21:56:59.284949 CHECKPOINT PASSED FOR HEIGHT 10000 <1ac1ebd25baf0d6ec593daa3389f1aa7e860ff2cc29f3cf1be586d245b379da4>
2015-Jul-22 21:56:59.518950 CHECKPOINT PASSED FOR HEIGHT 15000 <15567af42afc1ed00538f53b5e3822d421e3ed6372ca79f4ea4e3e3bab709a87>
2015-Jul-22 21:57:22.279390 CHECKPOINT PASSED FOR HEIGHT 175500 <3f7dd748b3b863b04654d87a387f2b65a365f467188971f3192eab2368e64a35>
2015-Jul-22 21:57:50.343839 CHECKPOINT PASSED FOR HEIGHT 450000
2015-Jul-22 21:57:52.247042 Blockchain initialized. last block: 467125, d74.h0.m25.s14 time ago, current difficulty: 1666761
(i plan to share my binaries but they're in testing stage yet)