Small black hard growth inside San Marzono tomatoes
So sorry for your problem with the tomatoes . This is called blossom end rot and appears as a dark, rotten spot on the bottom of the tomato. It may start out as a dime-size brown patch, then grow bigger and deeper, and eventually become covered with black mold.
As for preserving them quality is essential. Select only disease-free, preferably vine-ripened, firm fruit for canning/preserving.
From what I have researched and read as long as the tomato rot is removed completely and no black mold is present then they may be preserved. I caution you to make sure that no molds are present.
I hope this helps in your decision.
Eileen Haraminac Food Safety Educator