The symptoms you describe are quite specific, and they point away from cables, individual monitors, or a simple display preference problem.
The important clue is that the M4 Pro Mac mini recognizes whichever two displays are currently active, but will not maintain all three simultaneously.
Since you previously had all three working with the same hardware, and the problem began with a macOS upgrade, I would first verify the Mac's supported display configuration and then reset the display configuration rather than deleting preference files blindly.
For an M4 Pro Mac mini, Apple officially supports up to three external displays when using the appropriate Thunderbolt/USB-C connections, so three displays are not inherently beyond the hardware's capability.
The first thing I would do is check System Settings >> General >> About >> System Report >> Graphics/Displays with all three monitors connected and powered on. If all three displays are listed there, even though only two are actually showing an image, that would be particularly useful because it would distinguish a display-detection problem from a display-output/configuration problem.
I would not start deleting .plist files or using Terminal commands.
There is a safer diagnostic step: shut the Mac down completely, disconnect all three displays, start the Mac, log in, and then reconnect the displays one at a time, waiting several seconds between each connection.
This can force macOS to rebuild its current display topology without manually deleting configuration files.
Also check System Settings >> Displays while all three are connected.
Hold the Option (⌥) key; macOS may expose additional display-detection controls depending on the version. If the third display is detected but remains unavailable, that is more significant than simply not appearing.
One other thing I would specifically investigate is which USB-C/Thunderbolt ports the three displays are using.
On the M4 Pro Mac mini, the exact supported combinations matter. Because you are using three USB-C/Thunderbolt connections rather than HDMI, I would verify that your particular combination of Studio Display + two U2725 displays is supported by Apple's current M4 Pro display specifications rather than assuming that three USB-C displays are interchangeable.
Given that this started after the OS upgrade, I would check whether macOS 27.0.1/Golden Gate actually changed the supported display configuration or contains a display-related regression before attempting any preference reset.
That is something I would re-verify against Apple's current documentation and recent reports rather than guess.
Temporarily set both Dell U2725QE displays to 3840 × 2160 at 60 Hz. The U2725QE supports refresh rates up to 120 Hz, so this is a good way to rule out a refresh-rate or display-configuration issue without changing any system files. Dell UltraSharp U2725QE specifications