Hard to tell, the following is based on my own experience but as a rule of thunb, never edit a file in standalone mode, always use the project.pro. Except if it's not a hierarchycal file.
If you copy a project in order to modify it, copy the entire project. Keep the subsheets into the same directory as the .pro file.
When a sub file is created from the top file, a time stamp "U" is written inside the .sch file, making the file unique, Ref, Des and other fields are saved accordingly:
(this is for ver 5.15 but it should be the same for all the 5.0 to 5.19 versions):
$Sheet
S 8000 3400 850 300
U 6044F3D0
F0 "12-Configurable Extension Line Distribution" 40
F1 "12-Configurable Extension Line Distribution.sch" 40
$EndSheet
The sheets must have unique names.
If you use a unique subfile belonging to 2 diffferent projects _or_ if you edit it outside the project in standalone mode, you will change its contents and when called from the project, the behaviour will be umpredictable. Same if you decide to attach an already existing file to a project. I mean after the project has been closed, if you replace the sub sheet you just have created by another existing one.
I suggest that next time, when you have the issue, save the bugging .sch files in another directory, correct and save the prorject normally. Then compare the contents of the two equivalent sch files (modified and original), this will give you a clue where the issue is lying, especially if the time stamps are different.
Tpically, this an abstract of a .sch file called from several locations in a same hierarchy, after messing up with wrong Ref / Des:
$Comp
L !My_Switches:SW_SPST SW55
U 1 1 5A2DF87F
P 7700 2350
AR Path="/5A2E973C/5A31DD6B/5A2DF87F" Ref="SW55" Part="1"
AR Path="/5A2D3370/5A2DF87F" Ref="SW105" Part="1"
AR Path="/60419081/604568C1/5A2DF87F" Ref="SW?" Part="1"
AR Path="/604568C1/5A2DF87F" Ref="SW2024" Part="1"
F 0 "SW2024" H 7710 2490 50 0001 C CNN
F 1 "Key Switch" H 7750 2200 50 0000 C CNN
F 2 "~" H 7700 2350 60 0000 C CNN
F 3 "~" H 7700 2350 60 0000 C CNN
1 7700 2350
0 1 1 0
$EndComp
You can see the multiple time stamps sepatated by "/" as well as the multiple references. This may help to understand why your file remenbered the old organization.
And this is an abstract of a clean file called only once from the same hierarchy:
$Comp
L !My_Connectors_misc:GX12-6_inv J11
U 1 1 6092B577
P 2500 3925
F 0 "J11" H 2850 4125 39 0000 C CNN
F 1 "GX12-6_socket" H 3025 4050 39 0000 C CNN
F 2 "" H 2510 3726 39 0001 C CNN
F 3 "" H 2510 3726 39 0001 C CNN
1 2500 3925
1 0 0 1
$EndComp
Hope that it will help
PS have a look to this link:
https://forum.kicad.info/t/purpose-of-unit-path-entries-in-schematic/8254