Using PowerShell you can update the lookup list Id
$webURL = "http://server/sites/XY"
$listName = "MyList"
$columnName = "MyColumn"
$lookupListName = "Category"
$lookupWebURL = "http://server/sites/X"
RepairListLookupColumns -webURL $webURL -listName $listName -columnName $columnName -lookupListName $lookupListName -lookupWeb $lookupWebURL
Function RepairListLookupColumns($webURL, $listName, $columnName, $lookupListName, $lookupWebURL)
{
#Get web, list and column object
$web = Get-SPWeb $webURL
$lookupWeb = Get-SPWeb $lookupWebURL
$lookupWeb = Get-SPWeb $lookupWebURL
$list = $web.Lists[$listName]
$column = $list.Fields[$columnName]
$lookupList = $lookupWeb.Lists[$lookupListName]
$newLookupListID = "{"+. $lookupList.ID.ToString()+"}"
$newLookupWebID = "{"+$lookupWeb.ID.ToString()+"}"
#Change schema XML on the lookup column
$column.SchemaXml = $column.SchemaXml.Replace($column.LookupWebId.ToString(), $newLookupWebID)
$column.SchemaXml = $column.SchemaXml.Replace($column.LookupList.ToString(), $newLookupListID)
$column.Update()
#Write confirmation to console and dispose of web object
write-host "In Site" $web.Url "column " $column.Title "in Liste" $list.Title "is connected with" $lookupList.Title "from" $lookupWeb.Url
$web.Dispose()
$lookupWeb.Dispose()
}
Source - http://www.ilikesharepoint.de/2013/12/sharepoint-repair-lookup-columns-which-are-not-connected-to-a-list/