Instead of writing a long message, I will simply post a link to a video I created that demonstrates this exact issue.
Thank you for taking the time to watch the video and understand my issue. It's just too confusing to otherwise try and describe words.
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Show the clip that you move out of the way and back again in the Source panel.
It's hard to know what should happen when it's superimposed over other footage without knowing what that is by itself.
The clip, in this case, is just a PNG image of a logo. However, as I stated in the video the type of layer that it is doens't matter at all. It will happen to any kind of layer on your timeline, because I have had it occur with PNG's, JPEGs, MP4 clips, MOV files, Sequences, nested comps, Graphics that are created in premiere, Text layers... any kind of layer that Premiere will accept. Something I forgot to show in the video is that when I move the text layer on top of the smaller, PNG logo layere, the text layer remains just fine. But when I move the PNG back on top, it cancels out the text layer, beneath it.
What's on a higher track will cover anything below it unless you have a mask with lowered opacity on the upper track so show the lower track content through the mask.
If you are building a graphic, it's best to use the Essential Graphics panel in the Graphics workspace, and build it as one layer/item. You can add things like png/jpg to them, layer different elements of your graphic. Set opacity and such.
And then you have only one item to copy/duplicate/reuse as you wish.
You can have complicated graphics with logos and text and images sliding in and out separately.
Thanks for the response, Neil. Two things:
1: I don't really understand what you are referring to in your answer regarding the Essential graphics panel and creating a "one layer/item". Are you saying that you can take multiple items and somehow combine them in the Essential Graphics layer, in the same way that you might nest a series of objects (images, video, text etc.) or how you may create a series of layers in AE and combine them into a pre-composition? Is there a video or something you can point me to regarding this?
2: What you are suggesting is not providing an answer to the problem, I'm afraid. I have run into this issue again in an entirely different project. Again, I had a layer on the timeline that was visually disappearing on screen when another layer on the timeline appeared beneath the previously mentioned object's timeline layer. Also, as mentioned in the video I posted, the reason I know that this is clearly some kind of programming glitch is because these layers always start off working together in complete harmony with each other, and then for some reason, while continuing to work in that project, those layers started to behave this way. Sometimes closing Premiere and reopening it solves the problem, I would say about 45 -50% of the time. Otherwise, it doesn't and I then have to resort to methods such as using Premiere's "Export Frame" feature to take screenshots of the layers that are disappearing and using those images in place of the original object on screen. I have noticed that it does seem like Nested Clips are the common culprit... which is frustrating because I usually need those nested clips to be modular, so having to basically export it as a video clip just to get it to remain on screen is tiresome and redundant. Anyway, thanks for the feedback, I guess.
Try switching the renderer in the Project Settings to Software Only.
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OK, on your next question video, don't keep explaining how it keeps happening, all these versions, etc... BEFORE you get to 'bing' @ 1:12:00
The question is on your logo, how big is that file, and does it have transparency. I just created a timeline, put a shrunken png at the end and text underneath and all seems well, as you are expecting.
Show the size of the logo and display it by itself.
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I don't understand building that text/logo on separate tracks, but then, we all work differently. And at times there's good reasons for different methods.
There's a good question in this thread about the size & nature of that logo graphic. Answering that could help.
Personally, I'd use the Edit tab of the EGP for building anything like this. The text would be on one layer, the logo on a layer above them. Makes it possible to animate one or more layers by grouping them, and the whole thing separately. Among other fun tasks.
And as to the alpha layer, it can make a difference as to whether it is "standard" or "premultiplied" ... which is another wonderful bit of apparently necessary knowledge. Ae folks can go on about the details of that for hours ...