Problem with samples missing in audio waveform

I’m using Cubase 7 on Windows 7, and am using a Scarlett 18i6 interface in case that’s relevant to this problem. If you need specific details about other things let me know.

Recently I noticed a bunch of odd clicks and pops appearing in various places in songs I’ve been working on. I initially didn’t think much of it since when working at quick latencies my monitors would occasionally pop and crackle. But then I noticed that the pops were in the exact same places every time. When I zoomed in on some audio tracks I saw immediately where the problem was. The audio was dropping out for extremely brief periods of time causing audible clicks. It’s extremely consistent in that it’s almost always exactly 5 samples. This is all over the place in my audio tracks. I attached a screenshot of what my waveforms are looking like to this post.

So my questions then:

1. What caused this?

These tiny drop outs were not present when I initially recorded the audio. Additionally I took several month long breaks between various sessions for the tracks this problem appears on while waiting for musicians to be available so I’m unable to pinpoint exactly when this problem showed up.

2. What exactly is happening here?

There are two possibilities the way I see it. Either sound has been removed from the audio or blank space has been inserted into the audio. I’m not sure exactly how to tell which of these it is. But if it is the latter then fixing it would be much easier. My approach to fixing the tracks is completely dependant on what exactly has happened to the audio. So I’m hesitant to set aside time for a long session of fixing stuff until I know the answer to this question. I don’t want to do more damage than is already there if I can avoid it.

3. What can I do to prevent it from happening again?

Self explanatory. Obviously I don’t want to have to deal with this again in the future.

4. How can I fix my tracks?
This is my most pressing concern since these projects are all of music for an album project which I would like to complete soon. I have already tried a few different approaches to fixing it. I’ve had varied success but I’m unsure which of these (if any) is the best solution. These are the approaches I’ve tried or thought of so far:

a) Zoom in on the waveform and use the pencil tool to draw in a new waveform overtop of the empty space - Since it’s just a handful of samples to fix it’s not always audible if I manually re-draw the waveform. I’ve had modest success with this approach. However in maybe a quarter of the cases I’m unable to redraw the wave satisfactorily and still get pops (even if they’re reduced a little bit, though occasionally this has made them worse). This is also an extremely tedious and time consuming method.

b) cut around the click sounds, duplicate neighboring pieces of audio, and crossfade over the problem spots - I initially started doing this but it ended up being even more tedious than redrawing the waveform, seems to have worse results, and is just a huge organizational mess with tons of tiny edits all over the place. I’ve more or less already eliminated this approach but I’m listing it anyway.

c) Zooming in on the waveform highlighting the 5 error samples and deleting them - If my problem is a case of empty space being inserted into audio then this would be a great solution. Deleting the samples would seamlessly reconnect the separated audio on either side. However if it’s not inserted empty space but instead the audio cutting out, and I were to start deleting little chunks of the track like this repeatedly, by the end of the track the whole thing would be pushed out of sync by the duration of however many samples I removed. So depending on what my precise issue is this could either be the best solution or a terrible solution. I’ve tried this method a handful of times already in spots where pushing something out of sync wouldn’t cause a problem, and it seemed to work. But I don’t want to knock a whole bunch of tracks out of sync.

d) Some sort of click removal software - I assume there are some good plug-ins that can do this? I don’t have experience in using plug-ins dedicated to this purpose (and don’t really have the budget to invest in new software) so I’m not sure if it’s a good option or not. Especially for the kind of clicks that I’m dealing with. If it’s a case of the audio cutting out and not blank space being inserted then this could be the best solution.

So depending on what the exact problem is I’m leaning towards either C or D. But I’m hesitant to move forward until I can be confident I can satisfactorily fix it. So if anyone has any answers to these questions, has any advice, or has encountered and fixed this issue before please let me know. Thanks!
cubase audio error screenshot.png

To help answer why it happened, maybe worth checking with LatencyMon, http://www.resplendence.com/latencymon , maybe something changed OS-wise or something …

That could provide help in figuring out why it happened. Thanks I’ll give that a try.
I did remember that I updated my audio drivers at a certain point in the middle of this project. Maybe that could have had something to do with it?

If you’re certain this occurred after recording, then an audio driver change can’t have any influence on it. Your two possible reasons to have it occur after recording can only be explained by plugins and bouncing afterwards (or other edits deliberatley performed). If Cubase was adding silence or removing sound on its own, there would be an outroar on these forums…

For the repair - if you have Wavelab, that would be the best editor to fix these things. If not, I think cutting the empty samples should be fine. You say it’s in some places, so if you cut, let’s say, 20 places of 5 samples each that would move forward the audio after it by 100 samples. Depending on your audio sample rate, that would be 100/44,100th of a second to 100/96,000th of a second. At the most, that’s 2.3 milliseconds - nothing to lose any sleep over.

Yeah I didn’t think it was likely to be a problem with cubase specifically, if it was then that would be a pretty enormous issue. I’m pretty sure something I did somewhere caused it and I still can’t figure out what. I don’t think it was a bouncing issue since it’s appeared on some tracks I haven’t even finished comping yet.
If it happens again on future projects (so far on my recent recordings it hasn’t happened) then maybe I’ll be able to pinpoint the source of the problem with more accuracy.

For now at least I think cutting the empty space will probably be what I’ll end up doing, I tried it on a few more tracks and doing this seems to have seamless results, so I’m thinking that it’s got to be added silence rather than removed audio. Depending on the tracks some have only a couple of these errors but a few others do have upwards of 20 or more. But yeah, doing the math on it still works out to be a pretty tiny length of time if I delete those samples so it shouldn’t cause any huge issues (hopefully).
I don’t have wavelab, but it’s been on my want list for a while so this could give me the push to finally check it out. If cutting out the empty samples doesn’t end up working I’ll give it a try.