That's just it KaleunMarco, it strikes Stock just as much as TMO, as much as RFB, etc. It is a Silent Hunter: Wolves of the Pacific issue that has been around since day 1, unfortunately... it is worse in some versions of the game, better in others, but that might just be my imagination, and reminiscing about v1.4 - where a transfer was a transfer, not a teleportation with the same mission assignment...
For fighting the symptoms, a Save every time before entering the spawning range of Home Port, or roughly 50nm out, will help with a possible recovery. The best thing to attempt to avoid the issue is to not shell-out to Windows, accidentally or otherwise, which is next to impossible with the way Win10 / 11 interrupts the OS user with advertisements, or "notifications" in the systray, rather often. Moving a deck gun from fore to aft or vice versa can also complicate the issue, but I don't think the problem has ever been "fixed" by anyone, least of all Ubisoft or their associates, but not for lack of trying by just about every modder out there...