The offending lines were:
connectivity_[return_idx].first = this->Generate(x, y, z, l);
connectivity_[return_idx].second = this->Generate(x, y, z, r);

The Generate function triggers a potential reallocation of connectivity_
due to a push_back, thus making the assignment operation writing to the
wrong location in memory.
The usual implementation of std::vector doubles the size when
reallocating. So if constructing rotamer groups frames etc. from scratch,
exactly one reallocation happened before the lines specified before. The
size of connectivity was then sufficient and no further reallocation
was necessary. In case of merging a rotamer group, we reset the tree
and connectivity_ already has a certain size, making reallocations
unpredictable. Long story short: Default sidechain reconstruction was
already safe before (if you're not using an exotic std::vector
implementation) but Merge might have caused an issue.