yes, you can use any field in common between two or more indexes to filter the visualizations at a dashboard, and there is an additional option in the "Stack Management > Advanced Settings" that allows you to ignore the filter if the field used is not present in the index that creates the visualization. By default it is disabled.
Ignore filter(s)
This configuration enhances support for dashboards containing visualizations accessing dissimilar indexes. When disabled, all filters are applied to all visualizations. When enabled, filter(s) will be ignored for a visualization when the visualization's index does not contain the filtering field.
Thank you for the replies. The problem was indeed a mapping conflict. The mapping for the field in both indices was different. They are now the same and it is working
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