A mixture of SW counter and WDT a possible solution ? From a FAQ -
Using the Watchdog Timer to Reset PSoC® 3/5LP – KBA89152
Last Updated: 02/13/2014
Version: ** Question: How can you use the watchdog timer (WDT) to reset PSoC® 3 or PSoC 5LP?
Answer: The WDT feature can be implemented in PSoC 3 or PSoC 5LP using the two APIs CyWdtStart and CyWdtClear. The hardware implementation of the WDT prevents any modification of the timer once it has been enabled. It also prevents the timer from being disabled once it has been enabled, which protects the WDT from changes caused by errant code.
The WDT can be used when there is a chance that a code might get stuck inside an interrupt. Please note that the WDT should be cleared using the API CyWdtClear to prevent the PSoC from getting reset. So in this case, you can write CyWdtClear inside the interrupt and if the interrupt is executed normally, the API will clear the WDT, preventing the PSoC from getting reset. On the other hand, if the code gets stuck inside the interrupt for a time greater than the watchdog period time, the PSoC will get reset.
Thanks Dana for the answer but finally I didn´t need more time than 3 seconds.