What is "BASH masters list"? Your load order only consists of active plugins, the ones which Bash puts the two hex numbers next to. The information in the save file corresponds exactly. If the formIDs in the plugin, as the game sees them, have changed, the game will either trash the information or pick up some other random item for which the ID now corresponds, neither of which is preferable.
In the Bash saves tab, if you click on a save file the far right frame in the Bash window displays a list that's supposed to show all the esm & esp files that were active in that save, with color coding to show which ones correspond to files in your current Data folder. It also shows original load order (in hex numbers) and load order of active mods in the current setup. The same info, excluding current load order, is shown by List Masters in the File menu. All the ArmoryLab 3 series versions could be updated to another 3 series without loss of contents. I did that for several versions in my old, lost installation.