Hello Carlos,
PVsyst simulations are limited to a maximum period of one year. Accordingly, the associated weather data file is also limited to one year, and any data beyond 365 days in a custom-imported file are ignored.
If your dataset covers more than one year, you will need to run separate simulations, each using its own corresponding weather data file.
Additionally, since your measurements contain missing data, I would recommend isolating the reliable and consistent measurement periods into separate files using a text editor. These cleaned files can then be reimported using the Import and Generate Custom File tool.
Best regards,
Eric