When a Dataset on a sqlite database is configured with wizard, some times show weird behavior. Any edit to dataset designer may result to dataset fail (automatically being removed from datasources pane) when try to save.
Visual Studio Dataset Save unexpected fail
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This behavior may be a result of a datatype mismatch. For example dataset confiuguration wizard, auto asigns system.datetime on sqlite-datetime type of a database column. This results to error because sqlite-datetime is either number (i.e. real) or string. Right click dataset from solution explorer to open in designer, correct any mismatch and save, seems to solve the problem.