Your Eppy code needs to run before the jEPlus code. One way to achieve what you want would be to use EPMacro code, which can be inserted by Eppy.

Extending on the code from your snippet (untested):

for wall in walls:
    if wall.Name in ext_walls_windowless:
        wall.Outside_Boundary_Condition = "## IF EVAL[#[Layout[] EQS TRUE] AND #[Floor[] EQS TRUE]]\r\nAdiabatic,\r\n## ELIF EVAL[#[Layout[] EQS FALSE] AND #[Floor[] EQS FALSE]] \r\nOutside,\r\n \r\n##ENDIF"
        wall.Sun_Exposure = "## IF EVAL[#[Layout[] EQS TRUE] AND #[Floor[] EQS TRUE]]\r\nNoSun,\r\n## ELIF EVAL[#[Layout[] EQS FALSE] AND #[Floor[] EQS FALSE]] \r\nSunExposed,\r\n \r\n##ENDIF"
        wall.Wind_Exposure = "## IF EVAL[#[Layout[] EQS TRUE] AND #[Floor[] EQS TRUE]]\r\nNoWind,\r\n## ELIF EVAL[#[Layout[] EQS FALSE] AND #[Floor[] EQS FALSE]] \r\nWindExposed,\r\n \r\n##ENDIF"

As I say, this is untested but I think it should work, at the expense of being quite unreadable. I think there's scope for some kind of extension to Eppy here to generate EPMacro code.

I wouldn't be surprised if Ivan Korolija orYi Zhang have worked out a better way of doing this though.

Ok, I may have come to a solution:

import os
from eppy.modeleditor import IDF
import sys
import math
from geomeppy import IDF

def make_adiabatic(c):
        print('converting %s into adiabatic' %c)
        c.Outside_Boundary_Condition = 'Adiabatic'
        c.Sun_Exposure = 'NoSun'
        c.Wind_Exposure = 'NoWind'
        print('done\n')


# path to E+ idd file (required by eppy)
iddfile = os.path.join(sys.argv[4], 'Energy+.idd')
IDF.setiddname(iddfile)

# path to energyplus input file within each simulated folder
idf = os.path.join(sys.argv[2], 'in.idf')

# assigns reads parameter from jeplus
jeplus_floor = str(sys.argv[3])

# read idf file to eppy
idf = IDF(idf)

# Convert horizontal surfaces to adiabatic depending on the value of the jeplus parameter 
floors = idf_New.getsurfaces('Floor')
ceilings = idf_New.getsurfaces('Ceiling')
roofs = idf_New.getsurfaces('Roof')

if jeplus_floor == 'Ground_Floor':
    adiab_ceilings = make_adiabatic((c) for c in ceilings)
    adiab_roofs = make_adiabatic((c) for c in roofs)
elif jeplus_floor == 'Top_Floor':
    adiab_floors = make_adiabatic((c) for c in floors)
else:
    adiab_floors = make_adiabatic((c) for c in floors)
    adiab_ceilings = make_adiabatic((c) for c in ceilings)
    adiab_roofs = make_adiabatic((c) for c in roofs)

I look forward to receive your feedback on this!