If you remove a sync filter, the sync will only bring over records with a new system mod stamp (in Salesforce). For example, we had a sync filter on the opportunity object, for a lot of internal reasons, I couldn't mass update opportunities, I just had to "rip the bandaid" so to speak and de-activate the sync filter. All of the ops that were technically visible to the sync, just not synced via the checkbox didn't flood my system - this is b/c this system mod stamp wasn't recent. I was able to work with support to get them to adjust the time frame the sync was looking at for the opportunity object.
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