Activating and Chasing are separate activities.
For an activation you log everyone you work, it doesn’t matter where they are or what they are doing. They don’t have to be following any of the rules an activator follows for a valid SOTA QSO.
When you chase someone, they are activating a summit and following SOTA rules, you log them if you think they are a valid SOTA activation. Your status as valid SOTA doesn’t matter for a chase.
For a summit to summit contact, you both have to be following SOTA rules for it to be an S2S contact. That has to be the case because you are both activating a SOTA summit.
The S2S logging is an extension to chasing. So you log the chase and then declare it’s an S2S QSO by ticking the box and filling in the extra details. The software will actually enter a normal chase in your chaser log and it will enter an S2S contact in your S2S log. If you have already recorded the chase you will have received points and the second entry will be scored as 0. This is fine, the software can cope with this.
Or you can use CSV upload. In that case you can have your activation data, chase data and S2S data all in the same file. When you upload the CSV file as an activation, the activation records are found and added to your log. You then need to upload the CSV file again as a chaser log. Here, chase records are found and added to your log. Also S2S records are found and added to your log. Depending on how you add the data to your CSV file, you may see multiple chases for the same contact appear, only one chase scoring points. But as explained earlier, the software knows and understands what is happening.
To delete chases you can delete them from your chaser log. If you try to delete a chase that really is part of an S2S QSO you get told you can’t delete it from the current page. In that case, you show your S2S log and delete the QSO from there. That will delete the S2S and chaser data.