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Each case is unique but in general, the chimney should be done first. Special attention should be paid to the roof flashings around the chimney. If the flashings are behind the stone then make sure they extend far enough into the shingles so the new roof can be flashed properly. If the flashings are surface mounted and there is a counter flashing then the roofer should have no problem making the chimney base watertight
Our recommendation would be to do the massonry work first and then roofing for a few different reasons.
1.This gives the masons freedom to step and walk on the roof without causing damage to the new shingles.
2. You will want to make sure the new flashing that is intstalled around the chimney is installed correctly, accounting for any masonry changes and is not damaged due to installation.
3. Ultimately, that the new roof is not damaged and that the warranty does not get voided.
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