Alex,
I put this together in the hopes that you will see something I don't. If it helps great if not at least there is now more data to consider.
Two emails were sent to the box I am watch and I can see the data in the raw output from the section that watches for emails. Neither email had an attachment.

The next portion of the flow is the filter, the raw output was interesting in that it was minimal but I think this is what I would expect since there were no attachment. This is what the flow looks like
And this is what the output looks like

The decision resulted in a True condition which was expected, no attachments.
The first flow point in Yes is the Export email (v2) and I can see the body of the mail, all 35 pages, what I would expect to see if looking at the header and PDF code

The next point in the flow is the Create File and again it looks like I would have expected it
The next flow point is to create a PDF file from the output, I'm not sure this is successful, but honestly I have no idea what I'm looking at:
Notice the file content looks like a string of random numbers and letters.
And the final point in the flow looks like this

I was looking for something that might have indicated that there was a failure but nothing sticks out. Hopefully you might see something.
This flow is making me crazy. Crazy enough to look at the flow output from each step. Two emails were sent to the box I am watch and I can see the data in the raw output from the section that watches for emails. Neither email had an attachment.

The next portion of the flow is the filter, the raw output was interesting in that it was minimal but I think this is what I would expect since there were no attachment. This is what the flow looks like
And this is what the output looks like

The decision resulted in a True condition which was expected, no attachments.
The first flow point in Yes is the Export email (v2) and I can see the body of the mail, all 35 pages, what I would expect to see if looking at the header and PDF code

The next point in the flow is the Create File and again it looks like I would have expected it
The next flow point is to create a PDF file from the output, I'm not sure this is successful, but honestly I have no idea what I'm looking at:
Notice the file content looks like a string of random numbers and letters.
And the final point in the flow looks like this

I was looking for something that might have indicated that there was a failure but nothing sticks out. Hopefully you might see something.
Thanks Sam