import re
s = 'F6[ab]\nF3[ab]'
n = 'F6[ab]' # <= want to keep this in my string but want to change 'ab' in the new line
k = 'ab' # <= do not want to keep this in my string
c = '1' # <= change 'ab' -> '1'
print (re.sub(r'(' + re.escape(n) + rf')|\b{k}\b',
lambda m: m.group(1) if m.group(1) else c, s))
aW1wb3J0IHJlCgpzID0gJ0Y2W2FiXVxuRjNbYWJdJwpuID0gJ0Y2W2FiXScgIyA8PSB3YW50IHRvIGtlZXAgdGhpcyBpbiBteSBzdHJpbmcgYnV0IHdhbnQgdG8gY2hhbmdlICdhYicgaW4gdGhlIG5ldyBsaW5lCmsgPSAnYWInICMgPD0gZG8gbm90IHdhbnQgdG8ga2VlcCB0aGlzIGluIG15IHN0cmluZwpjID0gJzEnICMgPD0gY2hhbmdlICdhYicgLT4gJzEnCgpwcmludCAocmUuc3ViKHInKCcgKyByZS5lc2NhcGUobikgKyByZicpfFxie2t9XGInLAoJbGFtYmRhIG06IG0uZ3JvdXAoMSkgaWYgbS5ncm91cCgxKSBlbHNlIGMsIHMpKQ==