You will need to visit your Stash and select to Merge your Seasonal Stash into your Legacy stash. When merging Faction progress, the highest Rank between the latest Season, a previous Season or your current Rank in Legacy will be used for your Legacy Rank. (Faction Progress, Gold, Crafting Materials, and Stash items are all considered part of your Stash). 

To Merge, open your Stash and change the drop down in the top left to the previous Season then click the Merge button in the top right of the Stash window. 

If your Faction Progress is not transferring correctly, please try selecting a different Character and Merging the data again.