I want the party to know about the stronghold and the faction. It's more that I'd prefer a slow reveal in a perfect world and I was thinking that maybe the amnesia sequence might be one way to trickle the information in slowly and alert them to possible danger. The faction doesn't want the party to know about the faction.
The party has already encountered watch-beasts set to guard the periphery of the stronghold. And has some indication that the beasts are being fed by....something. They've also come across a slave outpost run by the faction, though they mostly avoided it and received little in the way of clues that it was any such thing.
One possibility might be to take it up a notch further:
Step 1 - the PCs (and players) meet the stronghold and faction as you've already proposed BUT as DM you ban the players from taking any notes of any kind during this sequence; which ends in some sort of fade-to-black moment (the PCs smell gas and then pass out, for example).
Step 2 - the PCs "come to" at some very-faraway and rather unsafe place with no idea how they got there and with only the players' memories of what recently happened. If asked, you-as-DM give NO clarifications or reminders of anything that occurred after they first saw (or entered?) the stronghold - they've got their player-side memory to go on and that's it; and wherever they are they've got other issues to deal with.
Step 3 - the process of getting from where they are to back home represents a big chunk of the campaign and involves a series of adventures, the intent being these adventures give the PCs enough levels etc. that by the time they get back to the stronghold they're somewhat capable of dealing with its occupants.
Step 4 - by the time they get back to the stronghold* the players' memories should be fuzzy enough that they can roleplay their PCs' quasi-amnesia about the place just fine.
Step 5 - after the PCs have dealt with the stronghold, or at some key point during this process when the PCs get their memories back, you update your player-viewable game logs to include everything that happened the first time they were there.
* - and if they never get back there or decide in the meantime to go different directions and do different things because one or more of the intervening adventures has captured their imagination then so be it; that's the DM-side risk here.