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You can not delete a "version" (or level) from Endevor, you can only delete the whole element (if that is allowed by your security and package approver rules if they apply).

Also keep in mind that when you move an element from one Endevor stage to the next Endevor stage, by default, Endevor will consolidate element levels.  Basically, this means that Endevor will move up the latest level.  For example, if you started with COBPGM1  1.00 from PROD, then made a change in DEVL it would be 1.01. If you made another change in DEVL it would be 1.02. And then if you made another change it would be 1.03, etc.  When you move COBPGM1 from DEVL to TEST, Endevor will "consolidate" 1.01, 1.02, and 1.03 into 1.01 in TEST. In this case, 1.01 in TEST was equivalent to 1.03 in DEVL. Endevor would then have no history of the intermediate 1.01 and 1.02 levels in DEVL.

So as long long as you are planning to move COBPGM1 from Stage A, you don't really need to "delete" your obsolete level. You could just retrieve the -1 level and add it back to Stage A. When it eventually moves from Stage A to Stage B, Endevor will automatically delete the intermediate levels.