I *do*/*will* have more to say on the issue, but the first thing is, never should someone apply the files provided (in this module by version) blindly. Yes, copying 1.5.3 files onto 1.5.4 files *will* remove functionality/action of the 1.5.4 files. They should always be reviewed/merged. If not mistaken the docs for this module even suggest the same... The important thing to know/understand/recognize is if the files being "replaced" have been modified by anything else... Something that has made installation of this module "easy" in the past has been the inclusion of the zc specific version of the file(s). Therefore the simplest of sites could blindly apply the plugin and continue forward without missing a beat. It is that part (to start) of this plugin that is missing for 1.5.4 and then any potentially needed logging associated with the added PCI compliance feature of 1.5.4.

Regarding "recovery" of existing/past uris, the data is all in the database and merely needs to be retrieved/handled at the right point in the code or .htaccess as identified above.