Here is an update on my end. I ended up having success placing the sde connection file in the same directory as the script and then referencing that with a system path variable. Here is a sample. This has been the most consistent method for me.
#Get script path
script_path = sys.path[0]
#Path to SDE using new script path variable
sdeconn = os.path.join(script_path, "SQLDB.sde")
#Path to feature class
polfc = os.path.join(sdeconn, 'ArcSDE.dbo.MyData)