Fix marking added item as 'to_update' #1389

Job	Run time
Spine Toolbox unit tests (3.8, ubuntu-22.04)	5m 12s
Spine Toolbox execution tests (3.8, ubuntu-22.04)	2m 24s
Unit tests (ubuntu-22.04, 3.8)	3m 8s
Unit tests (ubuntu-22.04, 3.9)	3m 18s
Unit tests (ubuntu-22.04, 3.10)	3m 16s
Unit tests (ubuntu-22.04, 3.11)	2m 59s
Unit tests (ubuntu-22.04, 3.12)	4m 10s
Unit tests (windows-latest, 3.8)	4m 47s
Unit tests (windows-latest, 3.9)	4m 50s
Unit tests (windows-latest, 3.10)	5m 9s
Unit tests (windows-latest, 3.11)	4m 45s
Unit tests (windows-latest, 3.12)	5m 27s
	49m 25s

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