To reproduce the issue:
1) Create a GenBank file containing the following data:
LOCUS seq1 features 16-JUN-2014 UNIMARK seq1 features FEATURES Location/Qualifiers misc_feature complement(1..9) /ID="test1" /Name="testName1" //
2) Open the file in UGENE
3) Outside UGENE append the following data to the file:
LOCUS seq2 features 16-JUN-2014 FEATURES Location/Qualifiers misc_feature complement(2..8) /ID="test2" /Name="testName2" //
(there is no UNIMARK line here)
4) Click "Yes" in the appeared dialog in UGENE
Result:
SAFE_POINT is triggered at src\corelibs\U2Gui\src\UnloadDocumentTask.cpp:186 "Trying to recover from error: Unable to restore relations between external objects! "
This issue was discovered during investigating a user request.