davyvy,
One approach is to simply clear the value of the cell and replace it with missing value (essentially same as delete). So..
:Value1 << Set Each Value( If( Value1[ ] == -99, ., Value1[ ] ) );
:Value2 << Set Each Value( If( Value2[ ] == -99, ., Value2[ ] ) );
I've found that Set Each Value is quite fast. I ran a test on a 5 column, 6.6M row table and each of the operations above completed in ~2s.
PDB