Those are good points. The email exchanges between Tipton and Elizondo on pages 37-39 (starting from 39 and reading up, as the replies are all top posted so the bottom is the first email in the chain) and then page 24 (with 24 coming next after 37) are the relevant ones in
https://documents2.theblackvault.com/documents/osd/20-F-0163.pdf.
The emails all took place over a short period between August 22nd and October 3rd. Sorry this is a bit long but I feel it's important to go through them understand the timeline and who knew what, when.
The first email (p. 39) Elizondo requests a "Program Meeting" about "our collective efforts" (Elizondo, with Stratton as the "Navy counterpart" perhaps) and Tipton accommodates.
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Then the next email (p. 38) Elizondo is saying he thinks Tipton can "take our effort to the next level". Then we have Elizondo speculating that Tipton had already guessed Elizondo was working on a "nuanced" effort, and had been when he had previously worked under Tipton, seemingly because Elizondo had talked about UFOs and video with Tipton (the Navy videos that Mellon later leaked to the NY Times?). Elizondo talks about his "portfolio" and a "facility" Tipton will be able to use (one of the Bigelow properties mentioned in the Kona Blue proposal?)
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Tipton's reply (p. 38) seems cordial for the vote of confidence, but confused by Elizondo's statements.
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Then we have Elizondo in a new chain (p. 37 and also 25 is a duplicate page) about an "Update" requesting further discussion and mentions a "friend of the program" Tipton will be speaking to. Tipton appears to confirm he will have a discussion with a person the next day and he gives his availability to discuss further with Elizondo (though the email header is cut off so we don't actually have the date when the reply was sent).
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Then a new chain from Elizondo (p. 24) about an unclassified draft letter. Most of Elizondo's email is redacted, but we can recover most of it from email included in a prior FOIA release (
https://documents2.theblackvault.com/documents/navy/DON-NAVY-2021-007793.pdf p. 29). The subject is "DRAFT DepSECDEF letter (UNCLASSIFIED)" and Elizondo mentions creating a draft letter, apparently umprompted ("took the liberty") to help Tipton take over responsibilities for AATIP. So Elizondo does mention AATIP explicitly. Tipton's reply is that he has not read it but will do so and reply with thoughts that day or the next. That's the last email, from October 3rd, 2017.
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In another FOIA document we learn from a memo from Garry Reid (Elizondo's boss, no relation to Harry Reid) that Elizondo abruptly resigned on October 3rd (
https://documents2.theblackvault.com/documents/osd/18-F-0324.pdf p. 8).
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Elizondo's resignation letter is terse (ibid, p. 6). He provides a longer "memo for record" on the next day (p. 7) stating his resignation is due to "beuacratic challanges and inflexible mindsets" about "further research" on "the phenomena".
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I think a plausible reading of this chain of events is that Tipton had no idea what Elizondo was talking about, and after realizing, he wanted no part of it (because he didn't believe, or he thought it was beyond his paygrade or need to know, or whatever other reasons), which caused Elizondo to resign in protest when Tipton did not want to help take their "efforts" and "portfolio" to the "next level".
On this interpretation, I do not see contradiction with Tipton's previous statement about himself and Garry Reid being unaware of any AATIP program while Elizondo worked for them. Tipton could have been using guarded language about exactly when he knew about AATIP, as Elizondo seemingly told him about it in the days leading up to his retirement, but wouldn't change the overall impact of the statement regarding Elizondo's official duties under himself and Reid.
This interpretation also does not require Elizondo to be explicitly lying. In a previous quote from Imminent regarding budget, he presumed that Tipton's old boss, Pede, had figured out what Elizondo was "really" working on, with a knowing wink. He may have sincerely thought Tipton knew about his "nuanced efforts" and was on board because of their passing chit-chat about UFOs.
Another option would be that Elizondo was intentionally leaving a paper trail, having already decided to resign and implement the plan with Mellon and Stratton. Chris Mellon's email (
https://documents2.theblackvault.com/documents/osd/20-F-0163.pdf p. 22) seems to be referring to the Tipton's emails (which are attached to his email) as a sort of leverage to get OSD/DoD not to push back on Elizondo's claims about AATIP.
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Whatever the case may be on Elizondo's motives, I don't find anything here convincing that there was a real funded program that Elizondo ran/worked for.