I'm sorry if this question has been asked before, but I did a lot of googling and haven't found anyone with exactly this problem. I'm running Lightroom CC 2015.3 on a Windows 7 machine, but I've had this problem since Lightroom 4.
I have a whole bunch of folders and subfolders set up in a publish to hard drive service. Some of them are smart folders and some are not; it doesn't seem to make a difference for this problem. All of them are set to resize and dynamically rename the photos upon export and are publishing to an external hard drive. It's a LOT of photos (probably around 20K--I have around 50K in my catalog but I'm not exporting all of them). Basically if I try to update published collections, or even when I initially tried to publish the whole set of folders, when I actually look at my hard drive and dig into the tree, I find that many subfolders had been skipped and in those that had been published, they often didn't have all of the photos in there. (In case it matters, these aren't particularly elaborate folder trees--I'm talking two or three steps in, max.) Inside Lightroom, there are no "photos to publish" left in these folders, so in order to get all the photos to actually publish, I have to go through and mark each subfolder to REpublish and publish them all separately. There are no error messages; I didn't even realize it was happening until I went looking for some of the photos. I can't seem to identify any pattern regarding when it works or not. It's pretty frustrating because now I don't trust it to work unless I do each folder manually, so it takes a lot of time.
Am I missing something? Is it just too many photos for Lightroom or my admittedly kind of crappy PC to handle? This feature is one of the main reasons I started using Lightroom, so I'd love to figure out what's going on. Any assistance would be greatly appreciated--thank you!!