If I fail a challenge, will that affect my ability to unlock things in the Fortress?

Question

I reached the Gore nest, and failed the challenge to get 3 unique glory kills on Pinkies. Upon repeating the level, I was unable to complete the challenges because I had unlocked all of the weapon mods.

Does this mean I cannot unlock everything in the Fortress of Doom?

And as a bonus question, how many of these challenges are only doable once?

Edit: to clarify, at the end of the level it grants a Sentinel battery to use in the Fortress of Doom, if you complete all three challenges in one level playthrough. When I played the first time, I got both Weapon Upgrades, but didn't complete the Pinkie Glory Kill Challenge, thus was not awarded the battery. The second time, I completed the Glory Kill challenge, but was unable to get the Weapon upgrades, since they are only "unlockable" once.

Answer 1

I'm not sure how having all the weapon mods affect your ability to glory kill pinkies. To complete the challenge. You must glory kill a pinky from the front, back, and side. Weapon doesn't matter.

Every challenge in the game is able to go back into the level and try again.

Answer 2

Ok, so I did a bit of investigating, and found the following information:

You need 22 Sentinel Batteries in total to unlock everything, including the Skins:

• Classic skin
• Praetor skin
• Sentinel skin
• Two Modbots
• Four Praetor Suit points
• Two Sentinel Shards

There are 18 to collect as part of exploration, the rest need to be gained from the Mission Challenges.

Mission challenges grant a total of 9 additional Batteries, totaling 27*.

Now, as for unlocking the Sentinel Batteries from the Mission Challenges, there are several reports about the "progress" being bugged, particularly when it comes to replaying the missions to complete missed challenges. However, this appears to simply be a bug:

We are aware of an issue where DOOM Eternal Mission Challenges show as being zeroed out when replaying a mission from Mission Select on the Main Menu or from the Fortress of DOOM. Please note that this is a UI error and you have not lost any progress. This will be resolved in the next update.

Source

So, to summarize; There are more than enough Sentinel Batteries to unlock everything in the Fortress of Doom, allowing you to miss up to 5 Mission Challenges, without missing anything. At least 4 Mission Challenges (3/3 in a single Mission) will need to be completed in order to gain access to all unlocks.

Additionally, replaying Missions may show a "loss" or incomplete Mission Challenge list, particularly when it comes to one-time unlocks, like Weapon Mods or Runes, etc., however a Battery will still be awarded if the other Challenges are completed (and a Battery has not been awarded for the level previously).

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^{*I have seen some sources say that the challenges reward 3 in total per mission, but I believe this to be a misinterpretation - 3 Challenges are required to be rewarded 1 Battery}