Selecting nearby polygons in QGIS?

I belive you would want to make a 50km buffer around the municipalities (as stated before). Once the buffer has been applied, you can open the attribute table and see which conservation units fall within the boundaries. You can then right click on the layer, Export, Save Feature As, select the format you want to save in (likely Shapefile), name the Shapefile (UCs, as you said), and click 'Save only selected features' under Enconding.

You mentioned wanting to maintain the attribute elements of the municipalities layer. In order to do this, I would frist perform a spatial join with the municipalities layer and conservation units layer. This would create one layer for both of them and will hold both of their attributes. Then, when you performed the buffer and exported the new shapefile, all of the details will be maintained.

I'm not sure about doing this in R, but using the arcpy package in Python is very useful and very fast. https://pro.arcgis.com/en/pro-app/arcpy/get-started/what-is-arcpy-.htm

If you scroll to the middle of the page, you can see examples and syntax of the arcpy buffer_analysis tool. It is relatively easy to navigate and, as I said, fast!: http://desktop.arcgis.com/en/arcmap/10.3/tools/analysis-toolbox/buffer.htm