Directional Light being controlled by Sequence different to the on being rendered.

I have a single level setup to render multiple sequences.

One of the sequences has a number of key framed changes to a directional light and a skylight.

When rendering other sequences, the lights are being controlled by the this sequence.

I have added the Directional light and skylight to all sequences and key framed there values at the start and the end of the timeline so they do not change, but this does not resolve the issue for all sequences.

The only workaround I have found so far is to mute the lights in the sequence that is causing the issue.

Does anyone know a more efficient solution?

Thanks