Indeed, once pig pen could be characterised by upheaval (6)
I believe the answer is:
yeasty
'upheaval' is the definition.
(I've seen this before)
'indeed once pig pen' is the wordplay.
'indeed once' becomes 'yea' (I can't justify this - if you can you should give a lot more credence to this answer).
'pig pen' becomes 'sty' (I've seen this before).
'yea'+'sty'='YEASTY'
'could be characterised by' acts as a link.
This may not be right. Some or all of it may belong to another bit of the clue.
Can you help me to learn more?
(Other definitions for yeasty that I've seen before include "Turbulent, restless; fermenting" , "Like taste of home brew" , "Fermenting or causing fermentation" , "Like a fermenting agent" , "having ability to rise?" .)