If this is running along the side of the house and not by the roof then maybe caulk at this point.
Flashing a fieldstone chimney along siding.
On each end of the pan flashing cut about 1 1 2 in.
The project is ocean front and it has become a point of discussion as to how to prevent water from penetrating when we get the sideways rain that we do.
Yes you can caulk but in reality you should also be using chimney flashing which gets attached to and sealed to the chimney and then gets bent over the j channel.
I ve looked around a bit and all the details i can find only deal with chimney roof flashing.
Once the pan flashing is in place nail it to the roof sheathing and lay the shingles over the flashing.
The first is called step flashing.
A second layer of metal is embedded in the chimney mortar joints and folded down to cover the top of the step flashing.
Proper flashing around a chimney includes two layers.
Next comes the counterflashing.
Along the bend at both ends so that the flashing bends around the chimney at the bottom and overlaps at the ridge.
Anyplace where the roof plane meets a vertical wall such as a dormer a chimney or a split level roof flashing is necessary.
The other measures should have been taken before the siding was installed.