Specs:
Mac m4 max
Sequioa 15.4
Illustrator 29.4

Bug:
In my illustrations I use placed JPG images within an objects opacity mask to add raster textures to different objects/shapes within the illustration. Often times, I am using the same image texture multiple times in different parts of the illustration so, I place it multiple times into the opacity mask of different shapes and scale, rotate, and position it uniquely for that object or part of the image. So, a green shape on the left and a red shape on the right will have the same texture, but each is a separate instance of the same image file placed within their opacity masks.

When opening files in 29.4 that were saved or packaged before updating (about 6 days ago) all instances of a linked file have moved to the same exact position, scale, and rotation on the artboard. They are still in their respective opacity masks, but often times not even over the object anymore, which makes them seem to have disappeared. So, if select the green object and red object and release the opacity masks, I have two instances of the same texture file stacked perfectly on top of each other in the center of the artboard. It is if any information about position, scale, and rotation was somehow lost.

As far as the linking goes, if I used an image 3 times, it appears 3 times in the links panel, and there is only one copy of the file in the links folder. So, all of that is behaving as expected. 

I rolled back to 29.3 and when I opened the same file everything is as expected.

Opacity mask disappears or scales weirdly after saving and opening document again. As shown in the pictures, the one named Original is what I saved with, all the bugged ones illustrate what happens every time I open the document. I just have to redo it all over again. In this case it's simple to solve, but I've had this happen with other more complex projects and it was annoying.

I can replicate the issue using the steps provided, thank you.
The rotated image with the opacity mask indeed has the placed PSD within shifted, for me way below I left it when saved the doc.

First of all thanks for the answers
Unfortunately I can't upload anything to this site anymore, every time I try to attach a file I get an error 422. So I can only tell you how to replicate the error.
Create a new CMYK file in Illustrator 29.4. Add a colored rectangle, use a 4-color psd as an opacity mask rectangle. Duplicate the rectangle itself in the same position. Select everything and rotate it. Save the file, close it and reopen it. If you save it with a pdf preview, the problem is also visible in the preview itself

@Mario, I have the .ai file but the linked files inside the .ai file, are missing. Please share the linked images also.

Thanks for the reply
Doing some tests I realized that the problem also occurs with files made directly in Illustrator 29.4. They seem ok until they are saved and reopened.
If I embed the images there are no problems, but when I unembed them the problem occurs again

Mario, do you mean opacity masks or clipping masks?
Can you share a file, please?
Also — when you save a file, do you check 'Include Linked Files' option or not?