Working with HoMM5 files.

In Photoshop, select the "Crop" tool, highlight the area you want to keep, right-click, and choose "crop." Then, in the "save as" menu, select the desired format (e.g., JPEG).
There are many programs for this purpose. For example, I convert using IrfanView with the Shell extension plugin (it's quick and convenient, and you can process files in batches), and I crop using the standard Picture Manager (from Office).

If I reinstall the game, will the saves be lost? :smile16:

No, they shouldn't – they are located in My Documents/My Games. But just in case, you can make a backup copy of the save folder :smile16:.

P.S. Regarding transparent pixels, Zubr is right; I didn't think about that :o. Picture Manager won't help with that.