Yes the primary side would be LV and should be tested at 500V d.c. and the secondary side SELV and tested at 250V d.c.
Where the SELV conductors cannot be removed from the transformer, as is the case with many used for downlights, the conductors are tested to earth at 250V d.c.
The difference between IR testing for initial verification and a periodic, is that with an initial verification, you would be expected to test during installation, before connecting any voltage sensitive equipment.
Obviously with a periodic, that would not be possible.
So you would have to either disconnect at least one of the conductors, or link out the equipment, or test with L&N connected together to earth, or in some cases use 250V d.c.
To prove separation between SELV and LV circuits, you would test between the live conductors of the SELV circuit connected together and the live conductors of the LV circuit connected together at 500V d.c.
There has been some suggestions that 250V should be used when testing between L&N connected together and earth.
To be honest, a fairly pointless exercise, as the point of connecting L&N together is to prevent the test voltage from flowing through the equipment.