This script can be use to rebuild the zebra DB. It stores all koha MARC records in iso2709, in the bilbios directory. After that, you just have to "zebraidx update biblios"
I tried on a 9900 DB, here are the results :
[paul@bureau migration_tools]$ ./rebuild_zebra.pl -c
9900
9903 MARC record done in 37.
9104120731354 seconds
[paul@bureau zebra]$ zebraidx update biblios
<snip>
18:31:24-11/08 zebraidx(20348) [log] Iterations . . . 144575
18:31:24-11/08 zebraidx(20348) [log] Distinct words . 39891
18:31:24-11/08 zebraidx(20348) [log] Updates. . . . . 46
18:31:24-11/08 zebraidx(20348) [log] Deletions. . . . 2
18:31:24-11/08 zebraidx(20348) [log] Insertions . . . 39843
18:31:24-11/08 zebraidx(20348) [log] zebra_register_close p=0x8104cf8
18:31:25-11/08 zebraidx(20348) [log] Records: 9887 i/u/d 9881/6/0
18:31:25-11/08 zebraidx(20348) [log] user/system: 531/145
18:31:25-11/08 zebraidx(20348) [log] zebra_stop
18:31:25-11/08 zebraidx(20348) [log] zebraidx times: 11.33 5.31 1.45