No - your config is stored seperately to the IOS .bin files, so you can update it without losing the config.
When you change the IOS, if a command in the stored config is no longer supported (or you downgrade the IOS to a version that doesn't support a command), the unsupported bits will not be loaded into the running config - so if you save it at that point you will lose the lines.
Until you save it again the config isn't modified.
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In normal cases -you use the IOS with the same features - when you upgrade your IOS it doesn't affect your configuration. To be sure please do a backup about your config to a separate tftp server (and also save your running config into the flash (nvram)). When you upgrade your IOS you just copy the new IOS into the flash and change the boot system image, so you don't need delete any files, if you have enough place on the flash for the new IOS image.
If some config options are not supported in the new IOS these lines of configs will be eliminated.
All in all make a backup for the worst case, but your config will remain.
Do a 'Show Ver" and look at the "Config Register" value. I believe it should be 0x2102.
Your router may be set to "ignore config" (commonly used for a password recovery).
You can verify this by entering "copy start run" from the enabled command line. It should load the stored configuration - including any active passwords(!) - if the startup config loads, make sure you have reset the passwords to ensure you'll be able to get back in.
Also if this works, you can restore the config register to the proper value with the confreg command in "config terminal" / "conf t" command line.
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