We have tested this issue with iGrd.NET+AFM 4.5.27 and iGrid.NET+AFM 4.6.0 in Visual Studio 2013 SP1. The problem does not occur.
We used these steps to update the components in the project.
1) Close any forms with iGrid and AFM in the designer.
2) Remove the references to the old grid and AFM add-on in the Solution Explorer (right-click on the Reference node like TenTec.Windows.iGridLib.iGrid.v4.6 and then the Remove command).
3) Add the references to the new iGrid (right-click on the References node, then 'Add Reference...').
That's all. If we reopen the forms with iGrid and AFM, check their localizable properties in different languages (by changing the form's Language property), all non-default settings remain the same.
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It's strange that your VS clears the localized property values. It should not happen. If you open the form resource file for any non-default language (for instance, Form1.es-ES.resx for the Spanish/Spain localization) in a text editor to see its contents, you'll see that the full iGrid or AFM version like 4.5.27 isn't specified anywhere in it, so this should not depend on the full version of the used components.