Two possible reasons a Luminate Online group mapped to a Raiser's Edge query might have less records than the original query include:
 

Not all the Raiser's Edge records are 'linked' to Luminate records

This function will only group up records that already exist in Luminate Online. It won't sync records that are only in Raiser's Edge to Luminate Online automatically.

You can query on Luminate Alias to check if this might be the issue. If you'd like to 'push' the Raiser's Edge records in your query that currently don't exist in Luminate Online to Luminate Online, you can use the 'Global Update' function.
 

Some Raiser's Edge records are organization records