Spot treating will kill the fissidens. Get the parameters in the right condition and they would just die off.
I have this experienced in my two tank. The fissidens mat I have had BBA on my 20G tank. I transferred them to my smaller tank which no algae and the BBA fissidens just turned red in few days and disintegrate.
"No CO2/poor CO2 & high light/ ferts = great way to grow algae" - Tom Barr