I didn't even bother to RTFA, because I see this every year or two when we're drilling big holes in glacial debris. It's about 50/50 between it being an artefact (anchor / piece of un-recorded piling / CIA Black Ops base) and a big boulder, because there are more artefacts in cities. but boulders are common enough.
Most of the time we drill through or round them, then cement the things in places ASAP. But sometimes they're more problematic because they tend to creep/ fall out of the walls and crush or trap later equipment at the most inconvenient possible time. Our normal response then, as a minimal cost / minimal risk strategy is to move location by 50 m and start again. On a tunnel-boring project, that could be much more of an issue.
But it's hardly unprecedented.
Ultimate solution : pull the TBM OOH (see, we have TLAs for this!), pump the cavity full of cement and let it set. Then drill ahead with a smaller probe drill (or several) to determine the extent of the problem. Apply sufficient quantity and placement of explosives to turn the big problem into lots of smaller problems. Tackle the small problems in sequence.