If my feelings or emotions are not desiring God then my faith is misplaced. Rephrased: If I'm not experiencing joy and peace from believing (Rom 12v13) then I'm not truly walking by faith (2 Cor 5v7). My faith at that time is the faith of a mustard seed and so it is faith that justifies (Rom 5v1) therefore this faith cannot be taken away (Rom 8v30), but the faith has been not been applied to the relevant promises of God resulting in false and evil emotions. Therefore I am not correctly dealing with my faith.
Eg Psalm 42v5: 'Why are you cast down, O my soul? And why are you disquieted within me?'
Problem: Bad feelings. Psalmist doesn't feel God. He's being introspective by questioning and analysing his experiences. What he feels contradicts what he knows.
His solution: 'Hope in God, for I shall yet praise Him'. The solution is a faith issue. He needs to hope in God. His mind dictates the solution for his heart to believe in. The mind understands but cannot trust. Hence Psalm 14v1 makes the fool out to be someone who declares in his heart 'there is no God'. When the mind trusts what it understands the heart responds.
Therefore feelings are more or less always linked to the application of faith. Where faith is wrongly applied feelings are wrong. When faith is harnessed securely to Gods promises joy floods the soul.
Example: Christan's worry. That's a sinful emotion (Phil 4v6). Worry is the not-believing that God controls all things for our good and His glory (Rom 8v28, Eph 1v11b). Therefore to overcome worry we need to believe the promises found in the texts above. We need to preach to our souls like the Psalmist did: 'Why are you worried O my soul? Don't you know that God controls all things? Hope in that!'.
I also believe that there are seasons with the soul. These are times when God doesn't work by the above rules. Sometimes we seek for intimacy with God and we don't feel it (Songs 3v1). John Owen claims that one of the reasons God does this is to make us seek Him with more energy and zeal.
On a similar topic I've recently read Jonathon Edward's 'Religious Affections' recently. It is amazing! I recommend it to everyone. He starts with the premise: 'True religion mainly consists in holy affections'. He argues that every action we do is based upon an emotion. If this is true then whenever spiritual duty is not delight we are sinning. This concept is majorly convicting.
In the words of John Newton:
Our pleasure and our duty
Though opposite before
Since we have seen his beauty
Are joined apart no more
To see the law by Christ fulfilled
And hear His pardoning voice
Transforms a slave into a child
And duty into choice