Unfortunately, this issue would be hard to debug without the save file, do you still have it or has it been overwritten? It would be located in “\AppData\Roaming\Godot\app_userdata\Angel Shell” on Windows.
Yes I still have it. Here are the contents:
{"clear_percent":0.0,"cur_biome":0,"current_chips":{},"discovered_areas":["(0, 0)","(23, 12)","(24, 12)","(24, 13)","(25, 13)","(24, 14)","(26, 14)","(23, 14)","(19, 11)","(24, 15)","(25, 15)","(24, 17)","(23, 17)","(22, 17)","(22, 19)","(23, 20)","(23, 19)","(23, 18)","(24, 18)","(25, 18)","(26, 17)","(21, 18)","(20, 17)","(19, 18)","(19, 17)","(19, 16)","(21, 16)","(1, 10)","(21, 17)","(21, 20)","(11, 14)","(19, 19)","(18, 19)","(17, 18)","(18, 9)","(17, 19)","(17, 20)","(18, 21)","(18, 22)","(16, 22)","(18, 23)","(19, 23)","(19, 24)","(19, 25)","(19, 26)","(7, 17)","(16, 26)","(15, 26)","(14, 26)","(15, 25)","(15, 27)","(13, 29)","(16, 24)","(15, 21)","(17, 24)","(18, 24)","(14, 21)","(14, 20)","(13, 20)","(14, 19)","(15, 19)","(13, 19)","(12, 19)","(11, 19)","(10, 19)","(10, 18)","(11, 18)","(9, 19)","(9, 18)","(8, 19)","(8, 18)","(8, 20)","(9, 20)","(12, 18)","(11, 16)","(12, 16)","(13, 15)","(12, 15)","(11, 15)","(10, 15)","(9, 15)","(9, 16)","(10, 16)","(-2, 12)","(10, 14)","(9, 14)","(8, 14)","(7, 13)","(8, 15)","(6, 15)","(6, 16)","(6, 14)","(7, 16)","(6, 17)","(5, 18)","(5, 19)","(6, 20)","(7, 20)","(9, 21)","(11, 20)","(13, 17)","(15, 15)","(13, 11)","(11, 11)","(11, 13)","(10, 13)","(9, 12)","(8, 13)","(8, 16)","(9, 17)","(14, 18)","(20, 15)","(19, 15)","(19, 14)","(17, 14)","(16, 14)","(14, 13)","(14, 11)","(12, 13)","(16, 16)","(17, 15)"],"held_weapon":1,"held_weapons":{"0":{"ammo":20.0,"exp":28.0},"1":{"ammo":20.0,"exp":8.0},"2":{"ammo":20.0,"exp":0.5}},"max_hp":3,"persistant_data":{"uid://bv73jc2qlqc0i":[["Npc3","Sequence"],["Npc","Sequence"],["Npc4","Sequence2"],["Npc2","Sequence"],["Npc5","Sequence"]],"uid://c1mavdpykvvs0":[["Npc3","SequenceDoorsOpen"],["Npc2","Sequence"],["Npc4","Sequence"]],"uid://csjdjr7r550qo":[["Npc","Sequence"],["Npc2","SequenceHasMap"],["Npc6","Sequence"],["Npc4","Sequence"],["Npc5","Sequence"]],"uid://ct007ycfchwc5":[["Trigger","(1344.0, 104.0)",true],["Npc","Sequence"]],"uid://dk6veutgjao5e":[["Npc","Sequence"],["Npc2","Sequence"]],"uid://ekoothc5ccji":[["Trigger","(1344.0, 104.0)",false],["Npc","Sequence"],["Trigger","(1344.0, 104.0)",true],["Npc","Sequence"]],"uid://m47n6gll4jlg":[["Trigger","(2272.0, -896.0001)",true]]},"scene_path":"uid://ekoothc5ccji","sequence_data":{"doors_open":true},"x":1450.0,"y":895.0}
Reading through it I'm guessing there's something about that first save room that initializes {"clear_percent":0.0,"cur_biome":0,"current_chips":{}} to these defaults.