You are making a mountain out of nothing here. There are no problems at all, these are just warning messages, not errors, and the functionality of the icons is guaranteed. Otherwise an error would be reported.
These warnings simply inform about a change in the parameters of a process. In this particular case, several parameters of the PhotometricColorCalibration process no longer exist in the current version of this tool. Since these parameters have been serialized in the icons file, the core application informs about this fact with the corresponding warning messages. This is an automatic response to a detected change.
PixInsight is an always-evolving platform. Existing process parameters may change, be removed or replaced with new ones when a process is undergoing intense development. This is perfectly normal and will happen again. In the current version of PixInsight we have implemented a new star detection engine, which is much more robust and efficient. The new star detector introduces many new parameters and changes the meaning of some existing ones (such as sensitivity, peak response and maximum star distortion). All processes that depend on star detection have been adapted to the new detector, which involves parameter changes in most cases. PhotometricColorCalibration and SubframeSelector are two of these processes.
We take our work very seriously when we release a new version of PixInsight, or of any of its standard processes or scripts. If we remove process parameters or replace them with new ones, we always try to guarantee that no breaking change will happen. When this is not possible, we in general have two options: either inform about the changes that can be expected appropriately (see for example the description of the new star detector included in the official announcement for version1.8.9-1), or replace the process with a new one.
Other applications try to hide information to the user. This has never been and is not our philosophy of development. Our style is exactly the opposite: we always try to provide as much relevant information as possible to the user. If in doubt, we always prefer to take the risk of providing too much information instead of too few. The fact that a process parameter has been removed and is not available when an icons file is loaded is relevant, hence we issue a warning message to inform about it. Understanding the information provided by our platform is essential to work with PixInsight.