Autoconfigure doesn't always work with USB to serial converters. Did you say you successfully downloaded a project to the PLC and then lost communication?
Normally, when you download a new program to a SLC and there are differences in any of the channel configurations, you will be warned and given a choice whether or not to apply those changes. Did you see this warning? If so, did you apply the changes? If the answer is yes to both of those questions, you should be able to look at the file you just downloaded to obtain the information required to properly configure your RSLinx driver.