If the portions are at the beginiing and/or at the end, you can trim the activity directly in Garmin Connect Web by removing the concerned parts. See the menu under the cogwheel symbol up right on the Activity page for the Trim option.
In the very worst case, you can export the file in the TCX file format and remove the offending points (certainly missaligned due to the drop of GPS signal) manually by editing the file in a common text or HTML editor. Notepad is just fine. The TCX format (unlike the FIT files) is humanly relatively easily readable, hence you do not need to be a computer geek for doing so.
Once edited, you can import it back to Garmin Connect (removing the original may be necessary).
Tried correcting like that as well as the Garmin fit repair tool but when I try to import I keep getting a response "We don't support the file type you tried to import"
