Hi!
In 1.9.4 we've introduced new "intelligent" mode for opening files. Looks like the option "merge with gaps" was lost. We will fix it ASAP. I've created an issue in the bug tracker: https://ugene.unipro.ru/tracker/browse/UGENE-526

Meanwhile you can do the following.

I've attached a simple Workflow Scenario which allows to read file with multiple genomes and merge them into single FASTA with Ns.
1) Open the attached file merge_with_gaps.uwl in UGENE
2) Set input path (file with your genomes) for "Read Sequence" element. You can do it in the Property editor (See attached screenshot). Make sure that mode is "Merge". You can set the size of a gap between sequences.
3) Set output path for "Write Sequence" element.
4) Click "Run"

After the schema is finished executing, open the result file in UGENE. It will be a merged sequence with exactly 100 Ns between genomes.

Fixed. Use any UGENE 1.10 snapshot with revision number >= 976 or wait for 1.9.6 planned to be released in 2 weeks.
http://ugene.unipro.ru/snapshot.html

OK.

This regression was introduced by UGENE 1.9.4, so even 1.9.3 must work

To get any old version of UGENE try to download the latest, replace numbers is the URL and download the needed one.