Yup, i always take it
Tried to get this one from Chongqing, and apparently I couldn’t keep it 
Sapper’s Axe: Mendoza, in Yates’s bedroom hanging on the wall
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Here is a list. Might be partial.
I haven’t checked all locations. As an example, the Sapper’s Axe might still also be in Bangkok
Melee Panel left
- Antique Curved Knife : New York, lockbox
- Katana : Isle of Sgail, exposition
- Burial Dagger : New York, lockbox (thanks @Beldingford for the correction)
Melee Panel right
- Mace : Isle of Sgail, Penthouse and Donation Room
- Circumcision Knife : Isle of Sgail, in a crate, in the Warehouse (credit to @Melusca)
- Tanto : Hokkaido, where the ninja entry is in story mode (if you spawn there), and in Yamasaki’s Room
- Sapper’s Axe : Isle of Sgail, Penthouse. Mendoza, Yates Bedroom
- Saber : Paris, exposition room
- Claw Hammer : New York, loading bay
- Amputation Knife : Miami, Emergency Bay (credit to @Melusca)
- Folding Knife : Ambrose Island, smuggling cave and in a tree next to the Hippie
- Police Baton : New York, ground floor security room. Haven Island, security hut (credits to @Agent_47 and @kyle)
- Baseball Bat : Whittleton Creek, Wilson’s office (the barbecue house). Hokkaido, Director’s Office
Rifle Panel
- Fusil G1-4/C : Ambrose Island, Milicia Soldiers
- Fusil G1-4 : Colorado, milicia Soldiers
- Tac-4 AR Auto : Whittleton Creek, Cassidy’s Armory
- Sieger AR552 Tactical : Mendoza, Elite Guard
- Fusil G2 : common,
- Shashka A33 : common. Marrakesh Soldiers, Ambrose Island Pirates
- Shashka A33 Covert : Dubai, Elite Guard
Shotgun Panel
- Bartoli 12G : Sapienza, at the top of the Ruins Tower
- Tactical Bartoli 12G : common. Paris security room
- Bartoli Hunting Shotgun : Dartmoor, under glass, corridor next to the Entrance Hall
- Golden Sawed-Off Bartoli 12G : New York, Vault, 47 needs to steal the seven goldbars while wearing the Bank Robber disguise
SMG Panel
- DAK X2 : Whittleton Creek, Cassidy’s Armory
- HX-7 : common. New York Elite Guard
- HX-10 : common. Paris Bodyguards
- ICA SMG Raptor : Chongqing, ICA Elite Guards
- DAK DTI : Dubai, Bodyguards (thanks @jan342 for the correction)
- DAK X2 Covert : Mendoza, Elite guard in the railing of the mansion (credit to @Olipro)
- HX-7 Covert : Whittleton Creek, one of Caddidy’s House Guard
Pistol Panel
- Bartoli 75S : common
- Bartoli 75R : common
- Hackl 9S : Whittleton Creek Guards
- Hackl 9S Covert : Isle of Sgail, buried in the sewers. Requires a Shovel, one can be found at the Old Oak Tree
Sniper Panel
- Bartoli Woodsman Hunting Rifle : Mumbai, Khashmirian’s Nest. Mendoza, Sniper’s Nest
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And here is a video illustration for the Hackl 9S Covert.
As far as I am aware this is the only place a silenced pistol can be found in the whole mode. In all fairness, it’s well hidden.
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I can confirm that Legendary Golden Sawed-Off Bartoli 12G can be obtained in New York vault. You need to do the Easter Egg, open the vault & collect all 7 goldbar while wearing bunny costume.
Also, Legendary Antique Curved Knife & Epic Burial Dagger can be obtained inside deposit safe.
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You guys haven’t listed the ultimate freeload: The money in New York vault
Or did they get rid of that?
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It’s still here. I posted it the general discussion topic :
And apparently, there is another in Santa Fortuna. The safe where El Matador can be looted.
Tiping that, I think I will have to check a few other Safes. Sapienza, Isle of Sgail come to mind.
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It’s still available.
You can also find it in Berlin, inside Rolf’s office.
In Sgail there’s also one of the two plague doctor knives (can’t remember which one) in one of the crates you can open as a custodian.
Edit: It’s the Circumcision Knife.
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Is there a reason you haven’t included the Assassin’s HWK21 Covert in this list?
There’ also a baseball bat in Miami, in the alley where Siera meets the blackmailer
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Just did a quick jump into the Safehouse to see if there are any changes, and the X2000 apparently does not have an allocated spot in the gun rack (it definitely had one in the CTT). Hence why you couldn´t keep it.
I´m a bit annoyed by the removal, since I was hoping IO would use this opportunity to finally give the gun a unique (supressed) model, as it is still the same like the G1 (probably the reason why it got removed, as it would essentially just be a duplicate gun atm). Hopefully they will actually do it in a future update, though my hopes are getting lower with every patch… 
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The Amputation Knife can also be found quite easily, in Miami, in the medics area near the head doctor.
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Imagine not getting it from Diana in the reward crate (the showdown ones) after completing a whole campaign.
Bruh i was expecting some legendary weapon or something, cheers Diana
At some point I grabbed the Claw Hammer from NY then promptly lost it when all the guards converged on my position after killing a target. Next syndicate I defeated, Diana rewarded me with that same hammer… Thanks Diana that’s gonna help me a lot more than the newspaper -_-
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Nice! My collection shall be completed and so all i need now are the weapons
In Yuki’s room (Hokkaido) there’s no longer a katana. But… there’s a tanto there instead 
Considering the katana can easily be found in the gigantic piñata that is Sgail, that makes it pretty easy to get a few different ninja weapons for the katana prestige objective (the description says it works with other ninja weapons than the katana, so I’m guessing the tanto and maybe the shurikens used in melee will do the trick too?).
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