I suspect that the problem is that the changes that are being made for you to make your application work are being made in the wrong place. From the sounds of things they are being made to configuration files that are regularly changed or updated by Plesk, and that's not really the best place for them as you've found out.
To get around this issue you need these changes that are being made for you to be added as a file that will be included into the configuration as opposed to changing the existing global configuration. There are specific mechanisms for doing this in Plesk - for example the use of the vhost.conf file to add or modify configuration options for a specific domain.
I use Centos myself, but I'm sure other Linux flavours have something similar: If I want to add a global configuration addition, for example to load a module like mod_deflate and the necessary configuration for it, I add it /etc/httpd/conf.d/my-custom-conf-file.conf
If for some reason the use of an include file just isn't enough for your particular application then all that's really necessary is to keep a copy of the custom configuration file ready to compare with the updated configuration file written by Plesk and merge the differences.
Having said that, on Centos I've not seen the global apache configuration file (which for me is /etc/httpd/conf/httpd.conf) being changed by Plesk and I do make certain changes to that file. I don't absolutely reply on it never being changed though.
Of course alternatively you might have found a strange bug - if you could let us know which file is being changed then it would help a lot