Whenever you are adding clips to the Timeline, try holding down the Alt key of the computer main keyboard to avoid disturbing the existing Timeline content including splitting of audio.
Have you tried right clicking the Timeline file for deletion and selecting "Delete" instead of "Delete and Close Gap" and then use the Alt modifier as you drag the clip(s) around with the mouse cursor?
Please give all that a look and let us know the outcome? But that Alt Key maneuver should work for you as it has for many others.
Ah, I tried alt before but it ended up just unsyncronizing the audio and video, I just have to push alt as I'm dragging scenes on top of each other, rather than holding alt before. Works like a charm! Thank you.
Thank for the follow up. Glad the suggestion worked for you.
Your mention of Alt key and unlinking audio from video brought back recollection of a thread to which I never did get a reply in this forum regarding Sync Linked Clips