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Second thoughts - the white residue could be mineral salts leeching from the mortar. Definitely not concrete cancer though.

No, imo the white residue is a separate issue to the waterproofing. As you say the white residue is blocking up the drainage points - perhaps the drains have been blocked for a long time, this has caused ponding on the roof resulting in the calcium residue? It's definitely not concrete...

The white would be calcium.. if you want to remove it yourself to mitigate further ponding and water damage, i'd use a scrubbing brush, one part hydrochloric acid, with ten parts water. As long as you're draining into a pvc pipe?