If I understand correctly, you have created a new sequence with an Equipment Profile and then changed some parameters in the Control Panel. You have assumed that these changes are saved within the Equipment Profile.
As you may have found, the changes you have made to the parameters are stored within the sequence file but not within the Equipment Profile. This is the expected behaviour.
If you want to amend the parameters and then overwrite these in the Equipment Profile you have to choose the 'Save Sequence as Profile' option under File. Or alternatively, Open the Equipment Profile, make the changes and then save.
Think of profiles as like a template, you apply this to a sequence and then any changes you make to the sequence using the Control Panel are particular to that sequence.