Blackssr, here are my findings so far concerning the problems you are having with RMIR v2.03 Alpha 25.
I take it that between
this original raw download of October 1 and
this completed one of October 23, the changes were made entirely with EZ-RC. I think this must be so as you were unable to use RMIR until I posted Alpha 25. My first observation is that the original one has a file length of 1341440 bytes, the completed one is 1783808 bytes. This difference is not due to your changes, but to EZ-RC having done something strange.
The original file has your Harmony icons represented without a transparency layer. It was this fact that caused many of the problems with Alpha 24g and which needed some substantial changes to RMIR to handle them. The completed file has them represented WITH a transparency layer, that layer marking every pixel as completely opaque. This adds one byte per pixel to every icon and is responsible for the great increase in length. The completed file also has the system icons for five of your devices changed. The icons are referenced by a single-byte value that labels the position of the icon in a table of system icons. In the completed file, five of these references have been changed, all to the same byte value that refers to a non-existent icon. If you load DenonAtmos into RMIR you will see that five of the devices have unchecked icon boxes. If you are still able to load the completed setup into your remote, you will see that these five devices have no icon. I have loaded it into my XSight Touch and have confirmed this fact.
Version Alpha 25 of RMIR treats your Harmony icons consistently, so when you downloaded your completed setup into it, it recognised the presence of the irrelevant completely opaque transparency layer on each Harmony icon and represented the icons without it. So although you made no changes, RMIR did so. (The reason that RMIR is able to handle every type of UEI remote is that it interprets the data when it downloads and reconstructs it when it uploads, so the display mechanisms handle interpreted data that is independent of the storage format in the remote.)
I have not been able to reproduce any errors from your files. I have loaded your completed raw download, all 1.78MB of it, into my Touch and confirmed the absence of icons on five devices. I have downloaded that, saved the result as a .rmir file and compared it with your DenonAtmos.rmir file. They are identical apart from a difference in the model of the remote (which is stored in the file). I have then uploaded this .rmir file to my Touch without error. After this upload I did a raw download and compared it with your "after success" raw download. They differ only in the five bytes referencing the icons for the five devices mentioned above. In my raw download they were the references to the non-existent icon, in yours they were to the correct icons. (I'm not sure what file it was that was successfully uploaded, but it appears to have been one with the correct icons.) Incidentally the "after success" and "after error" raw downloads you posted are identical.
So I can see no problems with Alpha 25 or your data but do see that EZ-RC has behaved erratically. Sequences of events that have caused a verification error on upload for you have not done so for me. This leads me to believe that somehow there is corrupt data in your remote. How it got there is unclear. You say that all your uploads were with Alpha 25, but the symptoms you experienced were similar to ones I had when I loaded your original raw download into my Touch with Alpha 24g. So my only suggestion at present is that you do an upload with Alpha 25, checking Help/About to be absolutely sure that it is Alpha 25 (however certain you are, please do this check), of the longest setup that has been in your remote. This should get rid of any corrupt data. Here is what to do. Please follow this precisely.
Download
blackssr_final_setup.rmir (it is in a zip package). It is the same link I posted before, but the file is different so be sure to download it again. Load it into Alpha 25. Open the Raw Data tab. You will see a table of hex values displayed in black, many of which are in boldface. The bold ones are bytes changed by RMIR. Open the Advanced menu and click on "Preserve original data". The display will turn blue (and is very much longer, if you try scrolling them down to the bottom). This is the data in your raw download of your completed setup dated October 23. Making sure that it is these blue values that are displayed, click the Upload up arrow on the taskbar. This should upload without any verification error. Close RMIR saying No when it asks if you want to save your changes.
This should restore your remote to the state before you started experimenting with Alpha 25 (and you can check that there are five devices with no icon, as explained above). Now try doing things again. If you still get a verification error on upload, or if you get one following the instructions above, please post THREE things. The file you were trying to upload, a raw download after the failure, and the rmaster.err file that you will find in the RMIR installation directory (you need to have closed RMIR before you can read or copy this). Post them in a single zip package to save space. Good luck.
BTW I have uploaded Alpha 25a to fix a bug reported
here. You may use this if you wish, but the bug it fixes is not relevant to your files.