Well, I've been doing some maintenance on my collection to try to week out dupes. Sometimes the issue is that I will download a movie, then see an uncensored version, and then see a sub-titled version! I tried to figure out which one was my preference. I notice that JavLuv will pick up all versions so one option is to simply keep them all. I did pick up about 320 GB of space!
That being said, the bigger deal is to replace a lower-resolution movie with a higher-resolution version. I notice that is one of the new features and that JavLuv will query you as to whether you wish to replace. Personally, I would like the option that once that query is made, there is a check box to "replace all lower resolution with higher resolution version." I'm lazy and like the global replacement. I suppose there could also be an option to "replace all lower resolution with higher resolution and delete lower resolution."
I'm very much opposed to a "do this for all files" automated option because this is a destructive operation. That is, you're allowing JavLuv to actually delete the existing movie(s) in your collection to be replaced with the new movie(s). The ID identification algorithms are, I think, fairly robust at this point, but there are still cases out there in which movies may get mis-identified, and with this option, it could accidentally lead to losing data.
So, given that there's no way I can guarantee 100% that JavLuv isn't actually mis-reading the new ID somehow, and therefore might replace your existing file with the wrong movie, it's very important that people actually check each file to ensure that's what they really want to do. Remember that JavLuv makes no distinction between one of your carefully curated and named movies it just hasn't scanned yet versus a random movie you just downloaded named orignsbkeroxxjvigms359qbqfbn7rtnwu1j31bin.mp4, which is pretty much guaranteed to produce an arbitrary (and incorrect) ID based on all that garbage filename.