Suite Search indexing

[محروم.كوم]

I upgraded from 3.8.4 to 4.0.6 and i have a large forum with many millions of posts and 300k members.
Search was not working so i tried to update indexes from the script and it gave timeouts.
So i ran searchindex.php copied from do_not_upload folder in shell.
I emptied the index and allowed it to index from 0, All working fine and it was running for around 10 hours and at the last it says "Re-Enabling indexes and repairing tables, please stand by ..."
After that SSH session got disconnected saying connection lost. I checked running 2nd time and same thing happens.

How to go through this final step?
I checked the script code and this last part giving trouble.

//////////////
if ($disableindex)
{
echo('Re-Enabling indexes and repairing tables, please stand by ... ');
$db->query_write("ALTER TABLE " . TABLE_PREFIX . "searchcore ENABLE KEYS");
$db->query_write("ALTER TABLE " . TABLE_PREFIX . "searchcore_text ENABLE KEYS");

$db->query_write("ALTER TABLE " . TABLE_PREFIX . "searchgroup ENABLE KEYS");
$db->query_write("ALTER TABLE " . TABLE_PREFIX . "searchgroup_text ENABLE KEYS");
echo("$vbphrase[done]\n");
}
$totalend = microtime(true);
////////////////////

I tried to run this using PhpMyadmin
from phpmyadmin,
ALTER TABLE searchcore ENABLE KEYS ran fine. but never said done, or any message saying completed. Is it ok? i tried several times same thing.

Aftar ALTER TABLE searchcore_tex ENABLE KEYS ran and it was running for like 15 mins and gave time out.

What can i do? __DEFINE_LIKE_SHARE__