I've seen a similar-ish issue, but for scanning wifi networks instead of BLE devices. Intermittent dropped BLE packets with AndroidBLEExample - #3 by jettonj
For me adding the SYSTEM_THREAD(ENABLED) seemed to help a lot, but that's of course not your issue here and just because I haven't seen it come back up doesn't mean its fixed. I'd be very happy if you find a solution!