There are times when there can be a need to run one of the QB Desktop utilities such as Data Rebuild or Condense Data. However, it should be noted that these utilities can cause the last modified flag on your records to update. For accounts with many records, this can end up being in the thousands. If you do not properly account for this, you could end up with an extremely long sync (on the next sync run) and/or the sync app can even crash while attempting to process that number of records all at once.

To avoid this problem, you want to cause the sync app to essentially "skip" those modified dates. Here is how to do that.

You will normally need to run QB Utilities in single user mode. Turn that on first to ensure that no other users can make changes while performing this procedure.
Once in single-user mode, run a sync and allow it to finish.
Close the sync app
Now run whatever QuickBooks utilities you need to run and allow those to finish completely. Note the exact time the utility completed and maybe add 2-3 minutes to that (for safety).
You can now re-enable multi-user mode in QuickBooks if you so choose.
Open the sync app and now manually change the last sync time for any data elements that are large (customers, invoices, etc). Change the sync time to the time you noted in step 4\. Again, you will probably want to add a couple minutes to this to be sure there is no overlap.
Once done, you can now allow the sync app to resume normal sync jobs.

What did we do here?

We essentially forced the sync app to skip the window of time where any QB utilities were running. The sync app therefore ignores any modified flags created by the utilities.
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