The more mortar you can eradicate from your roof the better, even installing dry valleys if your property has valleys. This mainly applies to Tiled roofs though, as Slate roofs sit pretty flush onto your valley lead and has such needs no mortaring at all.
The only other section of your roof left that has mortar should just be your chimney stacks, both the brick pointing and the mortar flaunching on top that holds your pots in situ or caps off your chimney top. But has part of your reroof guarantee this can be negotiated on a different timeframe to your new, fully dry, mortar free roof installation.
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