My brain hurts from trying to remember a problem I had with MicroWin about 10 years ago, but maybe it will help.
I had been debugging a program and hadn't been 'Saving' as often as I should. I got to the end of the day, went to shut down and before I knew what I had done I had clicked on NO when it asked if I wanted to save the changes. So I had a working program in the PLC and a non-working but fully commented program on my computer. I needed to fuse the two. I opened that latest version of the program and then uploaded the working program from the PLC and it fused the two. Most of the comments were in the right places, the only time I had an issue was where I had a empty network, the comments and network title were offset by the number of empty networks. I found that if I gave the network a title of any sort it fixed the problems. Now when I program if I leave a network blank for ease of reading I label it at 'Blank'. Just in case that finger goes to No instead of Yes to the save the changes question.
Bryan