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I do not think it is worth to seek an answer to the question "why".
Never edit template.css. For your custom code using custom.css (how to do it - read the Helix documentation)

yes, this happens after clearing the com_templates cache ... and I use custom.css too, but is inconvenient in some cases ... is it possible to disable overwriting for template.css ?

is it possible to disable overwriting for template.css ?

Yes, by setting file rights on your hosting.
But it is better not to do so. template.css - one of the key template files and update it should be opened for writing. In addition, you will have each time to change the rights when editing this file. I can not imagine a situation when editing this file is more convenient than the file custom.css