This bug has been reported before, where cameras that always reset to file number 0001 (or people who do that) sometimes run into issues importing the photos, and Lightroom sometimes get the files confused.
Are you sure this camera ALWAYS resets the file number to 0001?? There's not way to stop it from doing that? Seems to me that is the simplest solution, if it can be done.
If you have ExifTool, you can copy the Sony Date Time to whatever field is used by Lightroom for date/time. Also, you can have Lightroom NOT write the data to xmp until you get this straightened out, which will maintain the original EXIF.
Unfortunately I don't know of a way to stop this behaviour, though I hope Sony will eventually issue a firmware update to implement a more sensible file naming system. It's an absolute mess, since depending on the capturing mode it will use completely different systems of naming files. Not sure what they were thinking.
exiftool "-DateTimeOriginal<SonyDateTime" "*.JPG" fixes the date issue, though other issues such as wrong image orientation remain and can't be fixed.
I'll try to rename the files before importing, that way Lightroom shouldn't be confused. But there's still 6000+ files, some of which are affected and that I can't fix. :-/
Besides, it's not exactly speaking for Adobe if they can't get this issue fixed.
May I ask how old the bug is?
Sure you can ask. However, I have no idea.
I don't know anything at all about your camera. However, in the menu options for my Nikon camera I have a choice to have the numbering reset whenever I remove the card or have the numbering continue on. Are you certain there isn't such an option for your camera as well?
It's the latest Sony top of the line smartphone (well, apart from the XZ2 Pro), and Sony sadly wasn't so thoughtful as to give the option. It's a shame, because otherwise it's quite capable, despite the lack of OIS and missing raw support.
But regardless this is a bug that deserves fixing, since even if you have a camera that can be fixed, users will run into it the issue and lose some data. I noticed strange behaviour, but until I found out what happened...