Had what looks like a similar issue on a local EXT (file-based) SR, XCP-ng 8.3, sm-3.2.12-23.5.
Sequence: snapshot of a running Windows VM → disk resized (60 → 75 GB) → snapshot deleted while running. The VM froze.
SMlog showed the live leaf-coalesce failing on the parent resize, then reporting success anyway:
Expanding COW image virt size for VDI <parent>: 60.000G -> 75.000G
qemu-img resize <parent>.qcow2 80530636800
_doCoalesceLeaf: EXCEPTION util.CommandException, Operation not permitted
*** finished leaf-coalesce successfully
Leaf-coalesce failed on <leaf>, skipping
Afterward the VM wouldn't start (SR_BACKEND_FAILURE_46, stale tapdisk), the GC kept failing with HANDLE_INVALID for the parent VDI, and qemu-img info on the parent showed corrupt: true. Windows wouldn't boot after cleanup, so I restored from a veeam backup and moved on.
Hopefully the sm-3.2.12-25.1 fix covers this issue too.