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Michael, We are new to iSeries and I am just getting up to speed in WDSC. We will be migrating COBOL/DB2 programs from VSE to iSeries. The problem you described was one of the first I encountered and I consider it very serious. The IBM resource that has been assisting us suggested a circumvention, but that too has its set of problems. For the interim, the safest and least frustrating way that I've found is to open the spooled output from the compile that failed in a separate editor window and swap between it and the source window while fixing the errors. The good news is that this problem is getting more attention from development and I am expecting a fix very soon.
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