If I understand you correctly, you are using both Layer 1 and Layer 2 in the same measure - right?

And you are displaying Layer 2 notes in the measure, but hiding Layer 2 rests - right?

1) You can avoid the problem by entering all the notes in Layer 1, using the Speedy Entry Tool feature Voice 1 / Voice 2.

In that way you do not need to enter and hide rests - since Voice 2 can be launched on any beat in a measure, without having rests on the preceding beats.

2) If you must use two layers, flip each tie individually, with Special Tools Tool, sub-tool Tie Tool.

Wow!! Thank you so much! You're great!

yes, that was 6/8 beat and I captured only that part. 

Thank you again!! God bless you!!