Is there a way to have Audacity not only show clipping, but remove it in large cases? I have a few songs I’ve noticed were either making sounds they shouldn’t, or were becoming degraded. All of them showed a huge number of clipping. I’ve removed clipping manually from many songs, but this is daunting, to say the least. It seems like there should be a way for Audacity to repair the clipping it can show, quickly, and in massive amounts. If there isn’t a way, I guess I might have to start writing these songs off, as it is extremely time consuming. Thanks. 
If it sounds distorted, then it is probably too badly damaged to repair automatically.
There is a “Clip Fix” tool in Audacity. See here for how to use it, but don’t expect miracles 
http://manual.audacityteam.org/o/man/clip_fix.html
Yeah, thanks. I was afraid of that. I’ve used that Clip Fix tool, but it isn’t any faster than just doing it manually. The strange part of the last couple of songs I’ve found this way is that they still play fairly clearly. I’ve been combing my music library for old songs that might need attention, so that’s how I came upon these. When the clipping is showed, there are so many clip-lings that on one the song is almost completely red, and the other is just really loaded with clipping. Either way, it would take me days to manually fix them, or even use the clipping tool to fix them. Thanks. 
The red lines don’t mean that the audio is definitely clipped. It is a warning that the audio may be (and probably is) clipped.
If it sounds OK, then you can just use the Amplify effect (or “Normalize” effect) to bring the level down a little and it’'ll be OK.
A lot of modern recordings are maximized as loud as possible (see “Loudness War”). This can cause large parts of the audio to be very close to 0 dB. If the audio is then encoded in a lossy format such as MP3, that can cause the peak level to go a bit above 0 dB. This is because MP3 is not an “exact” representation of the original audio, but just a close approximation. When making an MP3 from an original recording, it is advisable to allow a couple of dB “headroom” to allow for this.
Because MP3 is a “lossy” (inexact) format, encoding always loses at least a little sound quality. If your recordings are MP3s (or other lossy format such as WMA or AAC) then probably the best thing is to just leave them as they are - although you may be able to fix the clipping to some extent, if you then re-encode in a lossy format, there will be further loss of sound quality, so the net result will probably be no better than you started with.
At the end of the day, your ears are your best and most important guide. If it sounds OK, then it IS OK.
For any type of “sound restoration”, it is always best to start from the best quality original that you can get. Preferably that will be in a “lossless” format such as WAV or a CD.
I tried something, on a hunch. I selected All, then went up to “Effects” and scrolled down to “Normalize”. Bingo, problem solved. I occurred to me that since clipping is a result of recording at a level exceeding parameters, that if the song could be returned to a normal balance, maybe the clipping would disappear. It did. I even had Audacity do another clip search, and it turned up zero. Cool. 
Just as the red clip indicators may be visible when there is actually no clipping, so there can be clipping without the red lines showing.
Here’s a couple of screen shots, first with clip indicators turned off, then with clip indicators enabled:
In the first labelled section, the waveform just touches the top an bottom of the track. It is not actually clipped, but is dangerously close to clipping. The clip indicators show the danger.
In the second labelled section, the waveform is clearly clipped. The top and bottom of the waveform are beyond the legal limit and cannot be reproduced by the sound card.
In the third section, the tops and bottoms have been clipped (chopped off) but are within the legal range (less than 0 dB) so there are no red warning lines, but it is still clipped and will sound distorted. Amplifying to a lower level does not magically fix damaged audio.
Because Audacity uses “32 bit float” format, it is able to handle signals that are greater than 0 dB, but sound cards can’t and most standard audio file formats can’t handle over 0 dB properly either. If, during the course of editing an Audacity project, the result of processing causes peaks to exceed 0 dB, then (providing that you are using the default “32 bit float” format), you can usually recover the audio without damage by amplifying / normalizing to a lower level (below 0 dB). However, if the audio was actually clipped when you imported/recorded it, then amplifying/normalizing to a lower level will just make it clipped at a lower level (like the third labelled section).
Flat tops/bottoms to the waveform when zoomed in close, are a visual give-away that the audio is clipped.
What you did was hide massive clipping so Audacity couldn’t find it. What’s saving you is the damage isn’t enough to be audible. If it was, you’d find that it didn’t go away.
Audacity flags clipping on the timeline. If the timeline doesn’t overload Audacity can’t find any damage.
I think the last change was overload damage had to continue for three consecutive samples before triggering the red bars. This was an improvement in the version before that which would flag normal effects by accident.
All you have to do is reduce any kind of damage volume very slightly and it stops triggering the red bars, but it’s still damaged.
I’m horrified that you’re walking away with the assumption that you can easily fix any kind of clipping with Effects > Normalize. Clipping or overload is when the digital sound channel loses its ability to follow the show. Tiny portions of the blue waves have nothing to do with the performance and that can’t be fixed.
Koz