Ah, this is NOT a runtime FME Engine thing. It is purely a workbench thing. We noticed during FME 2017 development that we were getting a few workspaces that had corrupted / misconfigured reader/writer settings in them. We believe this took place briefly in FME 2016s life and was triggered when someone would copy / paste a reader or writer. Basically the internal keywords we use *could* get mixed up in that case. While the original problem was cured long ago, there appear to be some workspaces out in the wild that have this. Now, if the settings on the two readers that were accidentally sharing an internal keyword did not conflict, there would be no problem. But we did see a few cases where there was a problem. We put in code to detect that situation and repair it, but decided we'd be a bit verbose in that situation.
If you want to know what gets changed, just do a text DIFF between the (backup) .fmw and the one you save after we say we did the repair. You should notice that the keyword prefixes are different in the reader/writer section. Other than that, there should be no material change (but...there will be lots of other diffs due to things getting reordered which happens most every time we save...but that is another issue).
Bottom line, this should be no issue at all and if anything things will only work better in FME 2017 -- but if you'd not noticed an issue previously then almost certainly there will be no actual behaviour change.
Hope this helps.