When a shapefile is loaded with another projection than the current, choosing "Reproject" create silently a new file with a new name. So if you edit the shapefile, it's not the original file which is modified but the new one. This is confusing.It's undertandable not to modify the original. At least, choosing "Reproject" should return a warning "This will create a new file < filename>" OK/NOK ?
The new file name is generated by adding projection name separated with dots. As an example, if you open batPub.shp, reproject will create batPub.RGF_1993_CC49.shp.
This is very confusing for the user but also for Qgis/Table Manager plugin because if you open batPub.RGF_1993_CC49.shp and use this plugin to modify fields, save will generate batPub.dbf, not batPub.RGF_1993_CC49.dbf, perhaps because it just get filename until it find a dot.
So I suggest
1) Not to use dot to generate new file name, rather use dash or underscore
2) ask user if he wants to save data into the same file name or create a new one when asking reproject.
I noticed that I have several shapefiles of this name copied into my D:\dev\Mapwindow5\bin\x86\Release folder that should be removed.