I really think any "re-encoding" to say VCD or SVCD is very counter productive. If you are going to spend all that time and effert re-building the ReplayTV mpgs you might as well get yourself a 50 dollar TV card and set up your pc to do the mpg capture real time. I've been in this capture game for a long time.
The extracted Replay Mpegs do have a bunch of problems. The least of which is the Sub-4000 units that have only 32 kHz audio.
By the way .. to "fix" the audio with Womble all you need is the Womble version dated November 2001. You can open up the audio dialog and change it there and then "save" your edits the normal way. No need to de-multiplex. It will re-encode your audio while saving the clip and the time is only a couple more minutes. (I typically do around 45 minute shows)
The Replay Mpegs were never intended to be used for "authoring" purposes. Only for play-back and viewing "as is". Of course this dosen't mean you can't try.
If this will help:
Most success parsing the entire mpeg through some kind of editor or multiplexing tool that has a real DVD profile. I use an "old" original version of TMPGenc. Under it's "mpeg tools" section there is a program called "VBV Optimizer". This is (I believe) a one step demux and remux utility. Just load the mpeg into it and the finished mpeg "mostly .. but not always" will be fixed. (make sure you select the TMPGenc Mpeg-2 Program stream)
After that parse, I bring it into womble and do my editing. Then in Womble I de-multiplex to elementary streams and use those as DVD asset material.
If the clip you are "cutting" has some kind of problem (broken GOP or what-ever) then the Womble sometimes has trouble joining at that point. If you were feeding the full multiplexed program stream to your DVD authoring program, during the import the program will stop. Look at the percentage marker and get an estimation of about where in the clip it bombed out. About 75 percent of the time you find it is where Womble joined your cuts. Remember, just doing a "save" with womble doesn't't change the mpeg. But Womble handles straight cuts and pastes differently than a cut and join with an "effect" inserted. So if you have that problem you can insert something like a "fade" or "merge" as the other poster suggested and Womble will be forced to actually RE-Encode those few frames. It doesn't add much time to the save as you are only encoding those few frames in and around the cuts and pastes.
That old version of TMPGenc is on my web site ... www.pcphotovideo.com
in the download area. It's one of the very first betas and has some English translation problems. I use it because the VBV-Optimizer works and is a one step process. Later versions of TMPGenc removed that utility and because of that you need to do a De-mux and then Re-mux.
Even with all that work .. (which really only takes about 15 total minutes with a fast CPU) you sometimes cannot fix all the problems.
FWIW, I've found the medium quality to have less problems than the Low or High.
But to take hours? to re-encode the Replay Mpeg to some other format (like VCD or SVCD) is really the wrong way to go about this. Like I said, you can get TV cards for 50 bucks or so, or even a higher end video/capture card for around 200 bucks and use that to record directly to VCD. SVCD will require some additional post capture "fixing" but for the most part the mpegs will work "out of the box". Without the ambiguity of the ReplayTV mpeg.