Recovering from a 502 due to disk space issues

We have migrated a huge repository (over 6,5gb) with binary files over to git-lfs, this includes rewriting the repository history.

We are currently experiencing that most of this data is still stored on the old filesystem, although we have configured a git-lfs instance. The new data is stored there as well, This leads to a huge problem, as it eats up twice the disk space of what it should.

Our hypothesis is that backups of this repository is causing the issues. Is this something we can delete safely? And how can we go forth to do so?