Thanks for the report. Using the latest publicly available download from April 30th, 2017 (http://mh-nexus.de/downloads/HxDSetup.zip
), I could not reproduce this bug, unfortunately.
I used LockHunter instead of Unlocker, because the latter was said to contain bundled software and be unmaintained now.
I created the following folder/file structure:
I installed HxD as portable in a new folder D:\HxDtest. Opened HxD32.exe per double click. Dragged in D:\HxDbugtest\folder1\b.txt from the explorer.exe window (with C:\Users\Maël\Desktop\HxDbugtest\folder1\ opened). Clicked the menu File|Save as, chose as target D:\HxDbugtest\bug\b.txt confirming to overwrite.
Then I closed the file, pressing x on the top right corner.
I did not change or edit the file before saving, scroll, resize or move any window of HxD (or the save file dialog) before or after save. Just hiding the main window (automatically) when activating the explorer window. I have child windows be maximized by default.
The results are shown in the following screenshot.
It might be that the file size is relevant of the dragged and dropped file and the replaced file.
If you could make a quick video, maybe the difference in procedure could be identified.