Rusty,
Let me start by saying that I don't use ShootProof. However, I use several Publish Service plugins from jfriedl (Zenfolio, Facebook, Flickr, and used to use Picassa). I use other PS's from various websites such as 500px, ImageRights and Instagram. I find the ones from jfriedl to be the best written and most comprehensive and the one from Instagram the least reliable. But, other than the basics of each such plugin adhering to the SDK for plugins provided by Adobe, each author chooses what features to include or exclude and much of that is dependent on the API capability at the other end. So, for example, Google's API does not include a way to modify an image after being uploaded so that capability can't be included in anybody's Google Publish Service.
So, why the ShtootProof PS tends to fail and require a re-install is almost certainly due to poor coding of the PS or a weak API at the website end or both. So, I can't be of much help there.
As any tool that tries to keep information synced between two systems written by different companies with different architectures and goals is a risky business from the outset. Of, course some work better than others. I'm very happy with the plug in's from jfriedle as they has been quite stable and error free for many years through many versions of LR. In most cases, where errors occur it is due to the folks at the website end changing or eliminating something that breaks the interface. One big one was when Facebook decided to not allow Image maintenance through an API from regular computers (only mobile devices). But, even so, due to such things being so complicated behind the scenes I also take care to protect myself in case one fails and things get tangled or wiped out.
What I do, as you alluded to, is to keep a parallel structure within LR of what is in the PS. I chose to use keyword hierarchies for this but collections could be used just as easily. Each time I add an image to a PS-collection (or whatever the PS calls it such as Gallery, Album, set, etc.) I add a corresponding Keyword to the image as well. When I remove an image form the PS I remove the Keyword. I am also reasonably diligent in verifying that the count of images in my PS collections match the count having the corresponding KW (Virtual copies are usually to blame when there are mismatched counts). You could do the same using dumb collections. Some PS plugin's allow you to create Smart Galleries or Smart Albums in the PS, but not all. Even though my Zenfolio PS allows Smart Galleries I choose not to use them so that I'd stay consistent in my methodology and workflow with other PS's that don't allow this feature. If yours does, then yes, having a dumb collection or keywords that indicate which images are or are not in the actual PS would be a way to reconstruct the PS if something got wiped out but this would most likely require deleting eveything from the ShootProof website (losing links, comments and what have you in the process) and then republishing it all.
piece of my Zenfolio Website PS
Corresponding keywords
Where possible, jfriedle has included a "sync" function but I tend to not use these as in practice, even a well written PS can only do so much and many times the value or key that LR and the PS rely on to match images on the website to those in LR is missing or doesn't match anymore. Because of this I tend not to use those functions of the PS. I have used such sync functions for an initial load of a PS from a website but it had a devil of a time finding the images in LR that were on the website even though they were there. This is probably due to my renaming files when I manually uploaded them to the website from LR Exports. As I recall, I gave up on this and using a split screen walked through the website images in one window while adding keywords for each website folder to each image in LR in the 2nd window. Then I cleared out all the previously uploaded images from the website and added them back using the PS by populating the folders in the PS using the Keywords. Since those initial loads, though, for the most part my PS's have behaved and I have not had to re-sync.
So, after rambling on perhaps a bit too much, I hope you get some useful info from this and sorry I can't help with your specific plugin.
Dan