Hey @Bryan @Matt C - I'm sorry for not updating this post. To close the loop on the matter and for everyone hitting this issue and landing here, it turned out to be an expected behavior by design that is documented here in the Note block: https://learn.microsoft.com/en-us/azure/logic-apps/workflow-definition-language-functions-reference#base64-encoding-and-decoding
Logic Apps - base64 function not shown in designer in subsequent edits

I'm using the base64 function within a Logic App like this;
Which is correctly shown in the code view like this;
However, if I come back to the Logic App and edit it later, the designer view shows this;
The code view correctly shows base64 is still there, but if you edit that action block, it is removed. It's all too easy for you to inadvertently break the Logic App with a future edit.
4 answers
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MikeUrnun 5,756 Reputation points
2020-06-03T21:02:44.277+00:00 Hi @Matt C - Thank you for raising this issue. I'm able to reproduce the issue in the Designer View, but for me, it persists the use of expressions under the covers in the Code View on all subsequent changes and saves between Designer and Code views. Nonetheless, I agree that this inconsistent UX in the Designer View is error-prone so I've created a work item to address this issue internally.
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Hatch 11 Reputation points
2021-07-23T15:57:27.347+00:00 I am also getting this issue and would be interested to hear if there is any update - unfortunately the Base64 function was stripped out and invalid data was written to a large number of files.
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Denis Skorski 1 Reputation point
2022-12-24T01:39:35.79+00:00 So, "Azure Logic Apps automatically or implicitly performs base64 encoding or decoding, so you don't have to manually perform these conversions by using the corresponding functions..." does not work all the time - the degree of frustration is ... well, very high.
What I found is that ALA strips off base64 / decodebase64 when these functions are the outtest in the expression. If you wrap your expression with, for example, concat(), ALA will not remove it.
Yes, it adds some overhead that might be considerable within "For each" actions, but it's better than getting frustrated more and more with how inconsistent Microsoft is.