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You need to set a Key Column(s) to have the tagged rows stay in place when saving your file. From the Help files:

Note: If tags are to be reapplied after reloading linked data, you need to specify key columns that can be used to uniquely identify the rows in each data table. See Details on Select Key Columns for more information.

To reach the Select Key Columns dialog:

 

 

On the menu bar, select Data > Data table properties.

 

 

On the General tab, click to select the data table of interest.

 

 

Click Edit, next to the Key columns for linked data field.

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