Citizenship: Is IRP needed to prove reckonable residence

So before the last IRP expired the applicant became eligible fore citizenship but applied for an EUTR1A application as they didnt want to leave their home countrys citizenship. Due to delays in EUTR application, the IRP expired and no temporary permission was given. There was an email trail and written letters asking for it regulalrly. This later helped them to get a CSEP. so one government wing has already accept it. The applicant stayed in country while the application was open. This was confirmed to them by the Immigration in an email that they could stay in country. Now they want to apply for citizenship but the calculator show they were out of permission for 4 months when they didnt had an IRP.

Is the delay in EUTR1A application due to which older IRP expired counted as reckonable for Citizenship? The applicant was eligible for citizenship before the IRP expired but die to delay and no temporary permission was out if IRP for 4 months. Specially if the applicant became eligible even before the IRP expired.