I would recommend against disassembling TI-OS to make modifications and then attempting to reassemble it. As others have mentioned I would recommend writing hooks and making sure they stay around through RAM clears.
If you really want to go the OS modification route so as to not lose it on a full memory reset. I would then instead of trying to build an 8xu from a modified version of the disassembly, write a patching program that patches the OS on device. I know a number of members have written OS modifications before for various reasons (fixing bugs etc).

I'm excited to see the final result of this. Good work so far @Ranman!

Cloudflare has not reached out to us and at this time we are going to treat it as we are not affected.
I'm moving this topic for now to general discussion.

To follow up on this, I received this email from cloudflare about the situation.

Dear Cloudflare Customer:

Thursday afternoon, we published a blog post describing a memory leak caused by a serious bug that impacted Cloudflare's systems. If you haven't yet, I encourage you to read that post on the bug:

https://blog.cloudflare.com/incident-report-on-memory-leak-caused-by-cloudflare-parser-bug/

While we resolved the bug within hours of it being reported to us, there was an ongoing risk that some of our customers' sensitive information could still be available through third party caches, such as the Google search cache.

Over the last week, we've worked with these caches to discover what customers may have had sensitive information exposed and ensure that the caches are purged. We waited to disclose the bug publicly until after these caches could be cleared in order to mitigate the ability of malicious individuals to exploit any exposed data.

In our review of these third party caches, we discovered data that had been exposed from approximately 150 of Cloudflare's customers across our Free, Pro, Business, and Enterprise plans. We have reached out to these customers directly to provide them with a copy of the data that was exposed, help them understand its impact, and help them mitigate that impact.

Fortunately, your domain is not one of the domains where we have discovered exposed data in any third party caches. The bug has been patched so it is no longer leaking data. However, we continue to work with these caches to review their records and help them purge any exposed data we find. If we discover any data leaked about your domains during this search, we will reach out to you directly and provide you full details of what we have found.

To date, we have yet to find any instance of the bug being exploited, but we recommend if you are concerned that you invalidate and reissue any persistent secrets, such as long lived session identifiers, tokens or keys. Due to the nature of the bug, customer SSL keys were not exposed and do not need to be rotated.

Again, if we discover new information that impacts you, we will reach out to you directly. In the meantime, if you have any questions or concerns, please don’t hesitate to reach out.

Matthew Prince
Cloudflare, Inc.
Co-founder and CEO

Python programming language for HP 49/50g (and TI 83/84):

Python4Calculators
http://py4calc.sourceforge.net/
https://sourceforge.net/projects/py4calc/
http://www.hpcalc.org/details/7800

Mind adding some more content to this post?
Like maybe some screenshots and talk about some of the details of how the implementation works?

That would be nice if you could compile an axe program straight into a 8xp file...

Technically that is exactly what Axe does.

First, please don't lock your threads. You have been getting help here, it's just that you haven't provided enough information for us to give you more help then we already have.
Second, please don't yell on the forums.
Third, if you admit that you were wrong, you probably should admit it there. I'm not the one making you look bad, you are making yourself look bad. Own up to your mistakes and attempt to learn from them.

Interesting thing about the crystal oscillators aging. I did a little reading into it, and if that is the case then you probably shouldn't have any problems with it doing what you are describing under normal use.

If you happen to get us some reproducible steps we will be able to actually triage what is going on.
Have you checked the backup battery to make sure it still has charge?
When you are editing programs and they seem to disappear are you editing them with the TI-OS editor or through some other program?
How are you determining the calculator's clock speed?
Could you elaborate on the following statement: "most of my RAM momentarily disappeared until I reset it"

Processors cannot run at faster speeds on their own over time like you are describing.

As for other settings being lost, could you check to make sure the backup battery still has power? It might not which would be why you could lose settings on a battery pull.

Also, from what I can gather from Cemetech, you have been playing with overclocking your calculator.

Is there a way to fix such issues without downgrading (patches and the like), or am I looking at something more sinister? I have had these and/or similar issues since 2015. I've been using 2.55 for years now.

I'm sure there is a way to patch the OS to fix it. It would require the issues being reproducible elsewhere though. Since others can't reproduce this they can't look into what the root cause is. You currently aren't giving us much to work with. I would recommend NOT garbage collecting after every file edit. Just let the OS garbage collect when it needs to, all you are doing is adding load to the flash chip. Making it's lifespan potentially shorter.

You mentioned that you were running your calculator overclocked, I would recommend returning it to the normal clockspeed. The OS and most programs are designed to work with 6MHz and 15MHz modes, and lots of times assumptions are made based on that when it comes to timings. This could be causing unexpected behaviour.