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PSoC Creator has an option to disable SWD during operation. This is done from DWR settings > System tab > Debug Select option
When this is set to SWD, the interface is always active. When set to GPIO, SWD is active only during reset.
You should be able to program using PSoC Programmer irrespective of this setting. Regarding JLink, I found this thread which seems to indicate an issue with older versions (<5.10p), where the device is not reset and thus SWD doesn't come up.