3 times this has happen -
I did the Scan of the 2 ships needed and are heading back to Paxius.
System Crashes and my mission is now:

1/1 Paxius Unstable Shipscanner
0/1 Underworld Nephil Scanned
0/1 Seraph Scanned
Explored Underworld: yes

Before the crash it was:
1/1 Paxius Unstable Shipscanner
1/1 Underworld Nephil Scanned
1/1 Seraph Scanned
Explored Underworld: yes

Because i had to go to absolution to find a Seraph to scan after underworld at least one of the Ships scanning should be 1/1 after the RB / Crash

there was a crash... this explains everything the bug is with the crash not with your mission

Just some more fact in this.

It 14 Jumps between Underworld and Absolution.

Scan Ship in underworld (Nephil)
Travel 14 Jumps to Absolution
Scan Ship in Absolution DG (Seraph)
Travel to Paxius

In 2 cases i did a Mission
Between Underworld and Absolution
and Between Absolution and Paxius
Both mission where done (Completed did not have to do them over again)

That show the RB on one case should only have 1 ship to scan in Absolution. RB time did not cover back the scan in underworld.

In the other case the mission i completed was after scanning the 2 ships
and heading back to paxius - as that mission was also not there to be done or do over again it show the RB should have had the 2 ships scan done.

All times the Exploring of underworld is done and it never went:
Explored Underworld: no

I think what is happening it the flags for the Scanning of the Ships get reset if you are logged off for some reason or log off.

Why do I say that?
1. did the missions and went to paxius and logged off.
2. had a 2nd account logged on – there was no RB
3. logged on to a Alt and played for about 1 hr
4. logged off alt and got on account waiting at Paxius with Heven? Hell? Completed ready to finish at Paxius base

And hear what happen:
1/1 Paxius Unstable Shipscanner
0/1 Underworld Nephil Scanned
0/1 Seraph Scanned
Explored Underworld: yes


Also a Seraph never shows up in underworld that I been able to see on 3 alts so far now.
So you have to go to Absolution to find one to scan

There was a rollback and weird things happen during rollbacks. It's not that hard to just go scan the ai again. You probably spent more time writing that then it would've taken to scan the ai lol.

And yes seraphs are in the absolution DG Penance.