Luminos,
Hard lesson to learn, but you will now know not to rely only on one particular check only. Same with controlling the mites - I don't rely on one 'winter' oxalic acid treatment to get them through the summer months, to the apiguard treatment after harvest.
My bees don't need any oxalic to get them through to the spring. They will get appropriate IPM controls throughout the summer - and not those expensive 'hive sanitisers', either.
I once bought two hived colonies with rampant varroa (at the right price, mind), just to free-up the apiary site. Lost at least one of them, but at least didn't have to worry about apistan strips being left in those hives all winter. I regularly check my colonies (not to see if they have varroa - I know they will) to estimate how heavy the infestation is.
You could try this next year. Collect a can-full (of nurse bees, mainly), roll them around with icing sugar and allow to stand, for a few minutes, over an OMF (or similar) grid, then allow them to run back into the hive over a white sheet. Compare the number of mites, left behind, with your other routine checks.
You may be surprised. Multiply up, to estimate the phoretic mites in the hive and then multiply that number by six to include all the rest (in the brood cells). By no means accurate, but may give you an indication of what you are looking for...
You might want to compare that figure with 'sugar dusting the hive frames' or whatever other checks you do (egs - natural mite drop checks, checking drone brood, even checking frames of bees for observable mites). It all helps to make you aware that any one check is not necessarily indicative of the true situation.
RAB