Hi,
Yes, it's easy to remove the click repairs from any particular section - highlight it, then right-click in the waveform display and choose 'Remove Corrections'. But before doing this, you might like to zoom in on a few of these apparently unnecessary corrections and inspect the waveform display. They are usually tiny, inaudible adjustments and it's easier just to leave them alone. The only time they might cause a problem is on certain types of percussion, in which case you might get some audible 'false positives'. Listen out for any dulling of percussive sounds, but if it's classical music this rarely happens. You will need headphones to hear it.
To convert a PP or BP marker into a click repair, click on it and press M to insert a manual repair over the top of it. Then adjust this as required (drag either edge). You need to do each channel separately. But this is rarely necessary on recordings in decent condition. VinylStudio does miss the occasional 'pop', but these are usually easy to see (and hence fix) manually.
It's worth saying that click repair is a trade-off between false positives and false negatives, and we're always interested in how our software performs. Send us some sound samples if you feel so inclined, details on how to do so on request.