Conquest points you've earned from Random Battlegrounds after the 4.3 patch was applied shouldn't be going anywhere.
Belfedere is correct, last season we got to keep the points earned during the "down week". Unless they state otherwise it is logical to assume the same will be the case here.
Edit: Found the post on twitter by Daxxarri here it is:@druidleaves @Bashiok If you got those Conquest point after the realms came up from maintenance, you should get to keep 'em.
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